Microbial body size is a critical biodiversity trait, determining microbial ecological roles. However, the relationship between microbial community-level body size and microorganism-driven ecosystem performance remains elusive. This study applied anaerobic digestion (AD) as a modeling ecosystem to explore the dynamics of microbial community-level body size and AD performance, as approximated by CH4 production, using amplicon sequencing of the 16S rRNA gene and 16S rRNA, and metatranscriptomic sequencing. Microbial community-level body size was positively correlated with CH4 production. This result stood on both the complex substrate (i.e., swine manure) and the relatively simple substrate by replacing parts of swine manure with fructose or apple waste. Larger community-level body size was coupled with higher microbial interconnections, higher functional diversity, and higher gene expressions in methane production and substance degradation. These findings provide evidence of microbial body size as a potential agent to predict and manage microorganism-driven function and service in diverse ecosystems.