Objective evaluation of innovation ability can be considered as an important prerequisite to improve the competitiveness of SME (small and medium-sized enterprise) clusters. Aiming at the complexity and fuzziness of innovation capability measurement, this paper presents a systematic evaluation model by combining fuzzy theory with analytical hierarchy process (AHP) which converts quantitative analysis into qualitative analysis. It mainly consists of four procedures: formulation of judgment hierarchy, establishment of judgment matrix, construction of fuzzy matrix and synthesis-evaluation. This approach is convenient and scientific and the results of an example indicate the system is feasible and effective. It provides theoretical reference for improving innovation abilities of SME clusters.