Allicin as an active component in allium species being widely present in food waste (FW) and waste activated sludge (WAS). Recently, allicin has been found to inhibit the anaerobic co-digestion. However, few literatures were available related to its impacting on organic matter release and microbial community in anaerobic co-digestion system of FW and WAS. Thus, this work aimed to fill that gap through use a series of batch test under conditions of pH 7 and 35 ± 1 °C. Experimental results showed that the anaerobic co-digestion system almost could not measure methane accumulation before day 20, when allicin dosage was 2.0 μg/L. However, the amount of intracellular material released from FW and WAS to substrate liquid was raised, including organic matter, PO43−-P and NH4+-N. Analysis of microbial community based on high throughput sequencing showed that microbial diversity increased at initial phase of anaerobic co-digestion from FW and WAS, meanwhile, community abundance of Candidatus_Methanofastidiosum raised significantly with co-digestion time. Whereas, methanosaeta abundance was only 19.74% in the allicin test reactor that it was the highest abundance in blank group.