With the change of national policy orientation and the rapid development of related industries, training high-quality innovative engineering talents has become an urgent task for engineering postgraduate education. In order to scientifically evaluate the innovation ability of engineering masters in China, an evaluation model of innovation ability of engineering masters is constructed and optimized based on the quality iceberg model, and an evaluation index system of innovation ability of engineering masters is established by using analytic hierarchy process (AHP) and entropy weight method, which covers 5 factor layers and 16 index layers, including innovative skills, innovative knowledge, innovative thinking, innovative personality and innovative results. Based on the evaluation index system, with 1821 engineering masters as the research object, cloud model technology is used to evaluate and analyze the overall level of innovation ability of engineering masters in China. The results show that: on the whole, the innovation ability of engineering masters in China is at a good level, but there are still some differences among individuals. From the perspective of various dimensions, the performance of master of engineering in the three dimensions of innovative knowledge, innovative personality and innovative achievements is relatively good, but in the dimension of innovative thinking and innovative skills, the performance is not good. In terms of various indicators, master of engineering has the best performance in the three indicators of comprehensive knowledge base, innovation achievement optimization and knowledge acquisition ability, while the weakest performance in the indicators of critical thinking, complex engineering problem solving and complex engineering problem raising, which needs to be further improved. Based on this, the following countermeasures are proposed: improve the evaluation system to promote the overall improvement of innovation ability of master of engineering, focus on the innovation skills and innovative thinking to strengthen its innovation ability, strengthen the innovation subject consciousness and function to realize the independent improvement of its innovation ability.