This study investigates the molecular mechanism of antihistamines in recognizing and regulating the histamine H₁ receptor (H₁R), a G protein-coupled receptor (GPCR) involved in various physiological and pathophysiological conditions. Using cryo-EM, the structures of H₁R in the apo form and bound to different antihistamines were determined. These structures reveal a deep hydrophobic cavity and a secondary ligand-binding site in H₁R, which may support the development of new antihistamines. Antihistamines exert inverse regulation by utilizing a shared phenyl group that inserts into the deep cavity and blocks the movement of the toggle switch residue W428. The results provide insights into GPCR modulation and facilitate the design of novel antihistamines. The study also explores the recognition mechanisms of three representative antihistamines—mepyramine, astemizole, and desloratadine—with H₁R. Mepyramine is recognized through a hydrophobic pocket and a conserved salt bridge. Astemizole occupies positions similar to mepyramine in the orthosteric pocket and interacts with H₁R through hydrophobic and polar interactions. Desloratadine is buried in the main orthosteric pocket and interacts with H₁R through hydrophobic and polar interactions. The structures reveal that H₁R has a secondary binding pocket, which can be exploited for the development of new antihistamines. The study also compares the ligand pockets of H₁R in different states and reveals structural plasticity in the ligand-binding pocket of H₁R. The structures show that H₁R adopts a typical inactive conformation in the apo state and that the high basal signaling capacity of H₁R may not be attributed to a preexisting stable open conformation of TM6. The study also elucidates the mechanism of H₁R activation, showing that the conformational changes in the extracellular region lead to different signaling outputs on the intracellular side. The results of this study provide insights into the molecular regulation of H₁R inverse agonists and a framework for optimizing a new generation of antihistamines. The study highlights the importance of understanding the structural states of H₁R and the interactions with antihistamines for the rational design of new drugs. The findings may lead to the development of more selective and effective antihistamines.This study investigates the molecular mechanism of antihistamines in recognizing and regulating the histamine H₁ receptor (H₁R), a G protein-coupled receptor (GPCR) involved in various physiological and pathophysiological conditions. Using cryo-EM, the structures of H₁R in the apo form and bound to different antihistamines were determined. These structures reveal a deep hydrophobic cavity and a secondary ligand-binding site in H₁R, which may support the development of new antihistamines. Antihistamines exert inverse regulation by utilizing a shared phenyl group that inserts into the deep cavity and blocks the movement of the toggle switch residue W428. The results provide insights into GPCR modulation and facilitate the design of novel antihistamines. The study also explores the recognition mechanisms of three representative antihistamines—mepyramine, astemizole, and desloratadine—with H₁R. Mepyramine is recognized through a hydrophobic pocket and a conserved salt bridge. Astemizole occupies positions similar to mepyramine in the orthosteric pocket and interacts with H₁R through hydrophobic and polar interactions. Desloratadine is buried in the main orthosteric pocket and interacts with H₁R through hydrophobic and polar interactions. The structures reveal that H₁R has a secondary binding pocket, which can be exploited for the development of new antihistamines. The study also compares the ligand pockets of H₁R in different states and reveals structural plasticity in the ligand-binding pocket of H₁R. The structures show that H₁R adopts a typical inactive conformation in the apo state and that the high basal signaling capacity of H₁R may not be attributed to a preexisting stable open conformation of TM6. The study also elucidates the mechanism of H₁R activation, showing that the conformational changes in the extracellular region lead to different signaling outputs on the intracellular side. The results of this study provide insights into the molecular regulation of H₁R inverse agonists and a framework for optimizing a new generation of antihistamines. The study highlights the importance of understanding the structural states of H₁R and the interactions with antihistamines for the rational design of new drugs. The findings may lead to the development of more selective and effective antihistamines.