In this study, the links between performance and microbial communities were investigated with municipal solid waste (MSW) at two feedstock ratios and eight organic loading rates (OLRs). The co-digestion systems were stably operated at OLRs of 2.0–6.0 g VS/(L·d). The performance of the co-digestion system varied with the feedstock ratio. Compared with the 50:50 (hybrid Pennisetum:MSW) system, the 75:50 system, GM31, obtained increases of 1.93–17.68% and 0.29–23.29% for the specific biogas and methane yields, respectively. Whereas a shift in bacterial and methanogen communities occurred as the operating conditions changed, particularly with OLR variations. The genera Saccharofermentans, Prevotella, Clostridium, Syntrophomonas, and Proteiniphilum became the dominant bacteria for the conversion of carbohydrates and nitrogen compounds as the OLR increased. Meanwhile, a shift from acetoclastic to hydrogenotrophic or multifunctional methanogens was observed.