Autism spectrum disorder (ASD) is a prevalent and complex neurodevelopmental disorder with a strong genetic basis. Although SH3RF3 has been identified as an ASD candidate gene, its biological function and pathophysiological mechanisms remain elusive. Here, we reveal that SH3RF3 functions as an essential scaffold protein that facilitates presynaptic vesicle docking. Mechanistically, it orchestrates the formation of a molecular complex between the kinase BRSK1/SAD-B and the ASD-associated active zone protein RIM1. Genetic ablation of Sh3rf3 disrupts this protein-protein interaction, leading to reduced RIM1 phosphorylation. This perturbation triggers synaptic dysfunctions, marked by a substantial reduction in both total synaptic vesicle (SV) density and readily releasable pool size, coupled with delayed SV replenishment kinetics. These deficits ultimately impair excitatory synaptic transmission in the prefrontal cortex, disturb the excitatory-inhibitory (E/I) balance, and elicit autistic-like behaviors in mice. Notably, prefrontal cortex-specific restoration of Sh3rf3 reverses behavioral and functional deficits in knockout mice. Furthermore, our characterization of the SH3RF3 interactome reveals a shared molecular network encompassing ASD-risk genes, indicating that synapse-targeted therapies may have broad applicability.