The effects of long-term fertilization on the functional diversity of the soil microbial community in tomato rhizosphere were studied. The goal of study was to provide scientific basis and theoretical guidance for the regulation of ecological processes in the tomato rhizosphere. In this study, soil was sampled from a protected vegetable field that had been fertilized for 29 years in Shenyang Agricultural University, and 11 treatments were chosen, including a no fertilization control (CK), and fields receiving nitrogen (N), phosphate (P), potassium (K), nitrogen phosphate (NP), nitrogen phosphate potassium (NPK) fertilizers, and their combined application with organic manure (MN, MK, MP, MNP, and MNPK, respectively). Biolog ECO-plate methods were used to analyze the soil microbial community functional diversity. The results showed that 1) organic manure significantly increased the content of soil organic matter, available P, available K, and available N, the application of N fertilizer decreased the pH of rhizosphere soil, and the difference in soil physical and chemical properties was significant. 2) The application of organic manure enhanced the ability of soil microbes in the tomato rhizosphere soil to utilize and improve the functional diversity of the microbial community. Among them, soil microbial use of carbon sources and microbial activity of the MNP treatment were the highest and greatest, respectively. Specific performances were as follows:① long-term fertilization changed the soil microbial use of carbon sources. The total utilization of six kinds of carbon sources was higher than that of single chemical fertilizers, and that of MNP was the greatest. ② In the six carbon sources, the utilization rate of amino acids was the highest, and the utilization rate of phenolic acid was the lowest. ③ Results of principal component analysis showed that there were 12 kinds of carbon sources with large contributions to PC1 and eight for PC2 out of 31 kinds of carbon sources. ④ Shannon index, richness index, and the dominance index of fertilizer treatments were higher than those without fertilization, but the uniformity decreased. The Shannon index and abundance index of MNP were significantly higher than that of other treatments. Based on all the results, we concluded that MNP fertilization was the best and could result in higher rhizosphere soil microbial functional diversity.