The assembly and specification of synapses in the brain are incompletely understood. Latrophilin-3 (LPHN3), a postsynaptic adhesion G-protein-coupled receptor, mediates synapse formation in the hippocampus, but the underlying mechanisms are unclear. This study reveals that LPHN3 organizes synapses through a dual-pathway mechanism: activation of Gα and recruitment of phase-separated postsynaptic protein scaffolds. Alternative splicing of *Lphn3* controls the Gα-coupling mode of LPHN3, resulting in variants that predominantly signal through Gα or Gα12/3. Gα-coupled LPHN3 variants impair synaptic connectivity as severely as the overall deletion of *Lphn3*. These variants also recruit phase-transitioned postsynaptic protein scaffold condensates, which are clustered by presynaptic teneurin and FLRT ligands binding to LPHN3. Neuronal activity promotes alternative splicing of the Gα-coupled variant of LPHN3. Together, these findings suggest that activity-dependent alternative splicing of LPHN3 controls synapse formation by activating two convergent pathways: Gα signaling and clustered phase separation of postsynaptic protein scaffolds.The assembly and specification of synapses in the brain are incompletely understood. Latrophilin-3 (LPHN3), a postsynaptic adhesion G-protein-coupled receptor, mediates synapse formation in the hippocampus, but the underlying mechanisms are unclear. This study reveals that LPHN3 organizes synapses through a dual-pathway mechanism: activation of Gα and recruitment of phase-separated postsynaptic protein scaffolds. Alternative splicing of *Lphn3* controls the Gα-coupling mode of LPHN3, resulting in variants that predominantly signal through Gα or Gα12/3. Gα-coupled LPHN3 variants impair synaptic connectivity as severely as the overall deletion of *Lphn3*. These variants also recruit phase-transitioned postsynaptic protein scaffold condensates, which are clustered by presynaptic teneurin and FLRT ligands binding to LPHN3. Neuronal activity promotes alternative splicing of the Gα-coupled variant of LPHN3. Together, these findings suggest that activity-dependent alternative splicing of LPHN3 controls synapse formation by activating two convergent pathways: Gα signaling and clustered phase separation of postsynaptic protein scaffolds.