Based on the long-term stationary field fertilization experiment in Yangliu of Anhui Province, principal component-cluster analysis was done of the data obtained with five types of soil enzymes (urease, acid phosphatase, neutral phosphatase, catalase and invertase) and seven items of soil chemical properties (pH, electric conductivity, organic matter, total nitrogen, alkalytic nitrogen, available phosphorus and readily available potassium) as evaluation indices, to valuate comprehensively effects of long-term fertilization on fertility of the lime concretion black soil at the experimental site. Results show that 2 principal components that could reflect 88.22% of the original information quantity without losing any original variables were extracted from the initial 12 indices. Within the primary group of principal components, ACP, NEP, EC, OM, TN, AN, AP and AK were the major contributors, while among the secondary group of principal components, URE, CAT, INV and pH were the major ones. As biological indicators for comprehensive evaluation of the fertility of Lime concretion black soil, acid phosphatase and neutral phosphatase were better than other three soil enzymes. Hierarchical cluster analysis of the new indices extracted based on scores of the two principal components revealed the effects of different patterns of long-term fertilization displayed an order of HMNPK, MNPK > M > NPK > CK, in other words, mixed application of organic and chemical fertilizer is the best fertilizing model, and followed by application of only organic fertilizer, as no-fertilization and application of solely chemical fertilizer could result in decline of soil fertility.