Microbial community functional diversity is a sensitive indicator of soil management, such as fertilization, especially long-term fertilization. In this paper, the functional diversity of soil microbial community was detected by BIOLOG system. The Average Well Color Development (AWCD) in BIOLOG plates indicated the ability of carbon utilization of microbial community. The indices of Shannon, Simpson and McIntosh were calculated to show the richness, dominance and evenness of the functional diversity, while the principal component analysis of substrate reactions reflected the main carbon sources utilized by microbial community. The results showed that all the treatments exhibited the elevation of AWCD during the first 72 hours of incubation, but the differences among the treatments were obvious. Both applications of organic manure mixed with chemical fertilizer and chemical fertilizer caused high increase of the AWCD while applying straw-incorporation and local traditional fertilization had less affection on the AWCD, which was even lower than the treatment without fertilizer. It was implicated that long-term fertilization resulted in the variation of the carbon utilization efficiency of soil microbial communities. The microbial community diversity indices were calculated based on the AWCD data at 72h and the differences among the treatments were significant. The treatments of organic manure mixed with chemical fertilizer and chemical fertilizer remarkably improved the richness, dominance and evenness of soil microbial community in comparison with the other treatments. Both treatments of straw-incorporation and local traditional fertilization induced increase of the richness and the dominance except the evenness which decreased compared to the treatment without fertilization. The nine principal components were extracted from the principal component analysis and their cumulative contribution of variance accounted to 85.73 percent. The variance contribution rate of PC1 and PC2 were 34.21% and 13.73%, respectively. The correlation coefficients between main substrates and PC1 or PC2 indicated that the main carbon sources for soil microbes were carbohydrates and amino acids in all treatments and there were significant differences of carbon substrate utilization patterns in different treatments. Therefore, long-term fertilization had significant affections on the functional diversity of soil microbial community, which, in turn, could induce variations of carbon and nitrogen composition of soil organic matter.