Autism spectrum disorder (ASD) is a severe neurodevelopmental disease with a high incidence and effective biomarkers are urgently needed for its diagnosis. A few previous studies have reported the detection of miRNA biomarkers for autism diagnosis, especially those based on bioinformatics approaches. In this study, we developed a knowledge-guided bioinformatics model for identifying autism miRNA biomarkers. We downloaded gene expression microarray data from the GEO Database and extracted genes with expression levels that differed in ASD and the controls. We then constructed an autism-specific miRNA-mRNA network and inferred candidate autism biomarker miRNAs based on their regulatory modes and functions. We defined a novel parameter called the autism gene percentage as autism-specific knowledge to further facilitate the identification of autism-specific biomarker miRNAs. Finally, 11 miRNAs were screened as putative autism biomarkers, where eight miRNAs (72.7%) were significantly dysregulated in ASD samples according to previous reports. Functional enrichment results indicated that the targets of the identified miRNAs were enriched in autism-associated pathways, such as Wnt signaling (in KEGG and IPA), cell cycle (in KEGG), and glioblastoma multiforme signaling (in IPA), thereby supporting the predictive power of our model.