Autism Spectrum Disorder (ASD), characterized by neurodevelopmental challenges, has observed a substantial increase in prevalence over recent decades, while the causative factors continue to remain elusive. Circular RNAs (circRNAs), a type of long noncoding RNAs abundant in neural tissues and intricately involved in neuronal development, have garnered attention as potentially influential regulators implicated in the manifestation of ASD. In exploring the molecular basis of ASD, we analyzed RNA sequencing and genotype data from ASD and control brains, specifically examining circular RNA dysregulation and associated trans-genetic effects. Using expression quantitative trait loci (eQTL) analysis, we explored the link between genetic variants and the transcriptional expression changes of circRNAs (circQTL) and distant downstream genes (trans-eQTL). Statistical analyses uncovered a pathway from genetic variants to circRNAs (circQTL) to genes (trans-eQTL) to ASD diagnosis, providing evidence for the importance of ASD risk genes in autistic pathophysiology. Furthermore, our results suggest that circRNAs play a regulatory role in ASD-related genes through interactions with microRNAs. Our framework and strategies are further validated by replication analysis in samples with schizophrenia. In summary, our work presents a framework to study the regulatory mechanisms in neuropsychiatric diseases and highlights the therapeutic potential of targeting specific genetic variants of circRNAs through DNA/RNA editing as an intervention for ASD.