In order to solve the problem of H2S corrosion in biogas utilization, it is necessary to understand the characteristics and mechanisms of H2S production in chicken manure anaerobic digestion (CMAD) and vegetable waste anaerobic digestion (VWAD). In this study, lab-scale batch tests of CMAD and VWAD were conducted for 67 days at 35 °C. The results showed that sulfide was found to be the major form of sulfur in CMAD (accounting for 90%) and VWAD (70%). The average concentration of H2S was 198 ± 79 ppm in CMAD and 738 ± 210 ppm in VWAD. Moreover, 81% of total H2S was produced at 20 days of methane production in CMAD, but 80% of total H2S was produced in the first day in VWAD because of the rapid production of biogas and fermentation acidification. The sulfide ion equilibrium model could universally and feasibly predict the H2S production in CMAD and VWAD. The abundance of Firmicutes, Bacteroidetes, Proteobacteria and Euryarchaeota accounted for about 95% of the total microbes in both CMAD and VWAD; the influence of the fermentation stage on the microbial community was greater than that of the difference between CM and VW; the abundance of SRB was 0.01~0.07%, while that concerning organosulfur compounds fermentation was 22.8~30.5%. This study indicated that the H2S concentration of CMAD biogas was more than five times that of VWAD because CM is alkalescent but VW is acidic.