Nowadays, strategic alliance has become an important choice to enhance firms’ market power. Set alliance firms as the research object, this paper investigated how the alliance firms choose their patent strategies and the realization of strategic and performance goals when taking the market motivation into consideration. Constructed the research framework of “market motivation-patent strategy-firms’ innovative performance”, we proposed the assumptions of influencing mechanism of market motivation on choice of patent strategies and the relationship among market motivation, patent strategies and firms’ innovative performance respectively. Take the alliance in IT industry as the research sample, we empirically tested the relationship among market motivation, patent strategies and firms’ innovative performance, and results show that: (1) difference in market position led to the difference in alliance motivation and choice of patent strategies, firms with low market power tend to choose the patent defensive and leveraging strategy under market access motivation, while firms with stronger market power would choose the patent propriety and leveraging strategy; (2) on the basis of alliance, firms’ patent strategic choice would influence their innovative performance, in case of market access, firms would enhance their innovative efficiency and market capitalization, while under the circumstance of stronger market power, the use of patent strategic profile only promotes their market capitalization, but have no effect on innovative efficiency or patent output at all.