Fertilizer efficiency directly affects the production of continuous cropping greenhouse cucumber. So analyzing the fertilizer efficiency is of great significance in providing decision-making support for fertilization of greenhouse cucumber. By establishing the DEA models of continuous cropping greenhouse cucumber and taking existing data samples as study objects, the problems of fertilizer efficiency in traditional fertilization, target yield fertilization and mathematical model fertilization were studied. And the technical efficiency, pure technical efficiency, scale efficiency and redundancy rates of the three types of fertilization methods have been obtained by analyzing the relationship of three inputs (N, P2O5, K2O) and one output (Yield). Through analyzing fertilizer efficiency of the three types of fertilization methods, it could get the sort by the size of mathematical model fertilization, target yield fertilization and traditional fertilization. The results showed that the method of mathematical model fertilization is more reasonable in fertilizing and the DEA method is efficient and practical in analyzing the fertilizer efficiency.