Exploring the mechanism of college teacher’s motivation effects on their research performance is very important for the innovation system of colleges research incentive. Through the 703 valid questionnaires from college teachers, the empirical tests of extrinsic incentive’s and intrinsic motivation’s effects on research performance are separately studied by using the path analysis of SEM (Structural Equation Model), based on the structural dimension analysis of extrinsic incentive and intrinsic motivation and research performance by EFA (Exploratory Factor Analysis). The results of EFA indicate as follows: 1. Extrinsic incentive includes salary incentive, evaluation incentive and promotion incentive; 2. Intrinsic motivation includes innovation motivation, achievement motivation, social motivation; and 3. Research performance includes process performance and result performance. The path analysis results are as follow: first, salary incentive, evaluation incentive and achievement motivation do not affect the process performance, while promotion incentive, innovation motivation and social motivation not only do but also further affect result performance by it. second, promotion incentive and social motivation do not directly affect result performance. Furthermore, salary incentive, evaluation incentive, innovation motivation and achievement motivation have the direct negative effects on result performance; and third, process performance(attitude and behavior) is the intermediate variable and key variable that can really make motivators work. The above results have certain reference value for the management reform of science research in Chinese colleges.