Temperature regulations (mesophilic/thermophilic) and digesting modes (mono-/co-digestion) play key roles in the biomethane potential of anaerobic digestion, but limited research focus on the synergetic effects on microbial interconnections of the biomethane process. In this study, the pineapple and maize residues under different operations were monitored by batch biogas assays and 16S high-throughput sequencing to explore: 1) biomethane potential regarding different operations, 2) microbial communities in different treated reactors, and 3) significant factors determine microbial distribution. Results showed that the co-digestion had higher methanogenic abundance and biomethane production (~3300 mL) versus mono-digestion under mesophilic condition. To the thermophilic condition, the co-digestion had less methanogenic abundance but more biomethane production (~5000 mL). Statistical evidence uncovered that the Clostridiaceae and Thermoanaerobacteraceae dominated pathways linked closely with methanogenesis which may contribute the more biomethane production in the thermophilic condition. This study demonstrated the temperature regulations drove rare taxa as major contributors for biomethane production.