Forest gaps play a crucial role in community succession and assembly in forest ecosystems; therefore, they have recently been recognized and implemented as effective forest management practice all over the world. Forest gaps are commonly created as small disturbances in secondary forests to improve forest regeneration, nutrient cycling, ecosystem functioning, and biodiversity. The objective of this study was to investigate the responses of the physico-chemical and biological properties and microbial communities in soil to different sizes of forest gaps—including small gaps (60–80 m2), medium gaps (130–160 m2), and large gaps (270–300 m2)—and to examine the driving factors that influence soil microbial community structure and composition. The results show that Gram-positive bacteria, Gram-negative bacteria, fungi, arbuscular mycorrhizal fungi (AMF), and actinomycetes were mainly aggregated in the gaps, and the structural diversity of soil microbial communities was related to the gap size (p < 0.05). The soil microbial community diversity increased and then decreased with an increase in gap size. Moreover, the effects of the available phosphorus, soil pH, soil water content, available potassium, nitrate nitrogen and ammonium nitrogen on changes in microbial biomass were significant (p < 0.05). The gap area and gap position and their combined interactions also had significant effects on soil nutrients, which impacts the soil microbial community. Medium gaps (130–160 m2) always significantly improved the availability of soil nutrients, and good management practices in secondary forests can provide effective microenvironments for soil microbes.