This study investigates the structural basis of antiphage immunity generated by the SPARSA system in *Geobacter sulfurreducens*. SPARSA is a prokaryotic Argonaute-associated system that involves a short pAgo protein and an effector domain, Sir2, with an N-terminal Sir2 NADase domain and a C-terminal APAZ domain. The SPARSA complex was purified and characterized using cryo-electron microscopy (cryo-EM), revealing a 1:1 stoichiometry between GsSir2 and pAgo. The cryo-EM structure of the SPARSA heterodimer shows that pAgo is tightly clamped by the N-terminal Sir2 and C-terminal APAZ domains, forming an armchair-shaped complex. The NAD+ molecule was observed within the crevice near the catalytic residues of GsSir2, indicating its binding site. The recognition of gRNA and tDNA by SPARSA was also studied, showing that the gRNA and tDNA are embedded in the nucleic acid-binding channel formed by pAgo and the APAZ portion of GsSir2. The gRNA and tDNA are fully Watson-Crick paired, with the first two bases of the gRNA forming an A-form-like conformation and interacting with specific residues in the MID domain of pAgo. The 3′ end of the tDNA is recognized by hydrophobic interactions with residues in the MID, PIWI, and APAZ domains of GsSir2. Molecular dynamics simulations revealed that the movement of a loop in the PIWI domain, triggered by the formation of the gRNA-tDNA duplex, allows water molecules to accumulate and facilitate the hydrolysis of NAD+. This study provides insights into the molecular mechanisms underlying the antiphage defense of the SPARSA system.This study investigates the structural basis of antiphage immunity generated by the SPARSA system in *Geobacter sulfurreducens*. SPARSA is a prokaryotic Argonaute-associated system that involves a short pAgo protein and an effector domain, Sir2, with an N-terminal Sir2 NADase domain and a C-terminal APAZ domain. The SPARSA complex was purified and characterized using cryo-electron microscopy (cryo-EM), revealing a 1:1 stoichiometry between GsSir2 and pAgo. The cryo-EM structure of the SPARSA heterodimer shows that pAgo is tightly clamped by the N-terminal Sir2 and C-terminal APAZ domains, forming an armchair-shaped complex. The NAD+ molecule was observed within the crevice near the catalytic residues of GsSir2, indicating its binding site. The recognition of gRNA and tDNA by SPARSA was also studied, showing that the gRNA and tDNA are embedded in the nucleic acid-binding channel formed by pAgo and the APAZ portion of GsSir2. The gRNA and tDNA are fully Watson-Crick paired, with the first two bases of the gRNA forming an A-form-like conformation and interacting with specific residues in the MID domain of pAgo. The 3′ end of the tDNA is recognized by hydrophobic interactions with residues in the MID, PIWI, and APAZ domains of GsSir2. Molecular dynamics simulations revealed that the movement of a loop in the PIWI domain, triggered by the formation of the gRNA-tDNA duplex, allows water molecules to accumulate and facilitate the hydrolysis of NAD+. This study provides insights into the molecular mechanisms underlying the antiphage defense of the SPARSA system.