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The soil profile is a strong and complex physicochemical gradient that greatly affects bacterial community structure and function between soil layers. However, little is known about molecular ecological network structure and bacterial community function under differing soil profiles in planted forests. Four typical native tree species (Pinus massoniana Lamb., Castanopsis hystrix Miq., Mytilaria laosensis Lec., and Michelia macclurei Dandy) plantations were selected from subtropical China as the research object. We evaluated molecular ecological network structure as well as potential function of the soil bacterial community at different soil depths (0–20, 20–40, and 40–60 cm) within native tree plantations. Our results showed that (1) compared to the topsoil (0–20 cm), the bacterial molecular ecological network scale increased within the middle layer (20–40 cm) and the subsoil (40–60 cm), and the interaction between species was stronger; (2) module hubs and connectors were the key bacterial groups in each soil layer and increased with increasing soil depth; (3) the dominant functional groups of the bacterial communities in each soil layer were chemoheterotrophy, aerobic chemoheterotrophy, cellulolysis, ureolysis, nitrogen fixation, and nitrate reduction, and they were related to soil carbon and nitrogen cycling; and (4) the different molecular ecological network structures along with relative bacterial functional group abundances among diverse soil layers were mainly affected by soil organic carbon (SOC), NO3−-N, NH4+-N, available phosphorus (AP), and total phosphorus (TP). Our study provides a theoretical foundation for bacterial community structure together with function within soil profiles of native tree plantations in subtropical regions.