To compare the efficacy and mechanisms of two microbial enhancement strategies—in-situ cyclic domestication and targeted screening/enrichment—in food waste residue composting, a 15-day aerobic composting experiment was conducted. Four treatments were established: an in-situ cyclically domesticated mature compost group (DF), a targeted-screening enriched consortium group (JJ), a commercial microbial agent group (EM), and a fresh distiller’s grains group (JZ). The differences in composting progression, humification, nutrient transformation, and gaseous emissions among the four treatments were systematically monitored and compared, and the underlying mechanisms were elucidated using high-throughput sequencing and co-occurrence network analysis. The results revealed a stark contrast in efficacy between the two strategies. The DF group exhibited comprehensive superiority: it rapidly entered and sustained a thermophilic phase (>50℃) for over six days, achieved the highest degree of humification (DP value of 2.63), and produced the greatest total nitrogen content (2.13%) along with the highest available nitrogen and phosphorus contents, while concurrently recording the lowest cumulative emissions of NH? and H?S. In contrast, the JJ group failed to reach the thermophilic phase, peaking at only 42.2℃. Its degree of humification (DP value of 2.23), nutrient retention, and emission reduction efficacy were significantly lower than those of the DF group. Microbial analysis indicated that the DF strategy successfully established a stable and tightly connected functional microbiota, with key genera such as Georgenia and Moheibacter identified as potential core members. Conversely, the JJ strategy enriched genera positively correlated with gas emissions (e.g., Bacillus), resulting in a loosely structured community suffering from niche dislocation. This study demonstrates that the success of a microbial enhancement strategy depends on preserving the ecological integrity and habitat-specific adaptability of the functional community. Furthermore, this research provides crucial empirical evidence and an ecological perspective for the development of effective bioaugmentation strategies for organic solid waste.