Forest restoration is a proven method to rehabilitate eroded soil. However, how the soil microenvironment of forest restoration affects microbial communities and soil fertility at the aggregate scale remains unclear, hindering the ecological well-being of development in the degraded lands in the Xishuangbanna region. To address this, soil samples were collected from a tropical primary forest (tropical rainforest, RF), an artificial monoculture forest (rubber monoculture, RM), and two restored forests (JRM: natural restoration of RM; JRC: natural restoration of RM with Camellia sinensis intercropping) and analyzed for soil physicochemical properties and microbial communities. Our results indicated that restored forest soils have higher levels of soil fertility compared to RM (i.e., SOC: 1.74–2.03 times; TN: 1.51–1.70 times; TP: 1.48–1.52 times), and the soil fertility increased as the size of soil aggregates decreased. The microbial alpha diversity and the complexity of microbial networks were higher in the restored forests than in RM. Microbial alpha diversity and co-occurrence network complexity increased as soil aggregate size decreased. These changes were significantly correlated with pH, electrical conductivity (EC), and soil fertility. Compared with fungi, bacterial network complexity was significantly associated with most soil fertility factors, and bacterial r-strategists increased in restored forests compared with RM. In addition, the random forest model and partial least squares path model further confirmed that forest types ( P < 0.05; total effect: 0.16) rather than soil aggregates ( P > 0.05; total effect: –0.07) significantly positively influenced soil fertility by inducing soil pH, EC, and bacterial communities but not fungal communities. These results suggest that forest restoration can foster conducive soil conditions that enhance the growth of soil microbes, especially the bacterial community, to participate in soil nutrient cycling and accumulation. However, JRC exhibited greater potential for increasing soil fertility than JRM, although both restorations played comparable roles in improving microbial community characteristics. In conclusion, the results of this study suggest that forest restoration in abandoned rubber plantations plays an essential role in improving soil fertility, but this depends on the restored forest communities and soil microbial community characteristics.