A pot experiment was conducted to study the effects of the endophytic fungi Phomopsis liquidambari strain B3 and Atractylodes lancea powder on rhizosphere soil microflora, enzyme activity, and available trace elements under continuous peanut cropping. The results showed that strain B3 and A. lancea powder significantly increased peanut straw and pod yield by 14.11% and 10.28%, respectively, relative to B3 treatment alone. B3 treatment significantly increased peanut root nodules as well as straw and pod yield relative to the control, which was grown under conventional fertilizer treatment. There were no significant differences in peanut root length and branch numbers between the treatments and the control. In addition, the B3 treatment resulted in significantly more culturable bacteria and actinomycetes in peanut rhizosphere soil at seed, podding, and mature growth stages than did the control. The B3 and A. lancea powder treatment resulted in a significantly larger population of culturable fungi and actinomycetes at seed, flowering, and mature growth stages than the control. 16S rDNA PCR-DGGE analysis showed that the B3 and A. lancea powder treatment significantly changed the soil bacteria community structure at seed, seedling, flowering, and mature growth stages and increased bacterial diversity during the seedling, flowering, and podding growth periods compared with the control, as estimated by the Shannon and band number indices. The B3 and A. lancea powder and B3 treatments markedly increased the activities of soil urease and sucrase during the flowering and podding growth periods, which promote material cycle and energy flow in the monoculture peanut ecosystem. It is worth noting that B3 andA. lancea powder activated essential trance elements (Mo, B, Fe, Zn, and Mn) in peanut rhizosphere soil at various growth stages and dramatically promoted absorption of Mo, B, and Fe in peanut leaves and kernels, particularly Mo and Fe. The results of this study suggested that the combined application of endophytic fungi and A. lancea powder could effectively improve the continuous peanut cropping soil microflora, promote enzyme activity, and increase the absorption of important trace minerals. These effects are important for minimizing or even eliminating obstacles associated with continuous peanut cropping.