The wide application of neonicotinoid insecticides in soil may affect soil microbial community, yet the information is limited. This study first reports the effects of thiamethoxam and dinotefuranon on soil microbial community. Soil from a forest land was collected and spiked with different nominal levels (0.02 mg kg−1, 0.2 mg kg−1 and 2.0 mg kg−1) of thiamethoxam and dinotefuran, respectively, and cultivated for 112 days. During the study, concentrations of the two neonicotinoids and their potential degradation products were monitored by LC-MS/MS. At day 112, the soils were analyzed for genetic profile by high-throughput sequencing and carbon metabolic profile by Biolog-ECO plate. The results showed that thiamethoxam and dinotefuran were both attenuated during the study with rate constants being 0.008–0.017 d−1 and 0.024–0.032 d−1, respectively, and biodegradation played an important role. As compared to the blank control, the exposure to the studied two neonicotinoids changed the microbial community, and the changes were influenced by both the type of neonicotinoid and the level of exposure. As compared to the blank control, the relative abundances of phyla Gemmatimonadetes and OD1 decreased under most exposed conditions, while the relative abundances of Chloroflexi and Nitrospirae increased under most exposed conditions. The community transition changed the functional potential, particularly carbon metabolism (mostly decreased) and nitrogen metabolism (mostly increased). As compared to the blank control, the utilization of total 31 carbon sources (including six categories) was increased under low exposure to thiamethoxam, but was decreased under all other exposed conditions. Low exposure to dinotefuran stimulated the utilization of three categories of carbon sources (amines, carbohydrates and phenolic compounds). Low exposure to both neonicotinoids increased the community diversity, while middle and high exposure to both neonicotinoids decreased the community diversity. These findings provide new insights into the effects of neonicotinoids on microbial community in soil. Display omitted •The persistence of thiamethoxam in soil was longer than that of dinotefuran.•Exposure to thiamethoxam and dinotefuran changed bacterial community genetically.•The genetic community transition changed the carbon source utilization profile.•Effect on soil microbial community was influenced by type and level of exposure.•Chloroflexi and Nitrospirae increased after exposure to both studied neonicotinoids.