The aim of this study is to examine the impact of strategic alliance partner characteristics namely (partner complementarity, partner commitment, and partner compatibility) on firm's innovation, which includes incremental innovation and radical innovation. The population of the study contained (13) Jordanian Pharmaceutical companies, and the sample unit consisted from (122) managers and head of divisions working in strategic alliances, marketing and production areas within the target companies. In order to gathering the data required for measuring the study variables a questionnaire was developed. The results of the study showed that the strategic alliance partner characteristics had a significant impact on the Jordanian pharmaceutical companies' innovation, and the impact of alliance partner characteristics (Compatibility, Capabilities, and Commitment) on incremental innovation is more than the impact on radical innovation. Also the results showed that the complementarity of partner has the highest impact on the firm innovation, then the compatibility, then the commitment. Based on these findings the study recommending that the companies that seeking for innovation through a strategic alliances must select the appropriate partner who has a complementary capabilities that contribute non overlapping resources to the relationship, and a partner who has the unique competencies; and the partner who has a compatible strategic objectives, organization culture and management style; and the partner who has a strong sense of commitment for the alliance.