In order to incentive the knowledge staff effectively, it constructs a total recognition rewards theoretical model of “compensation incentive - work recognition - personal growth” based on the development of incentive theory and practice, and conducts a questionnaire survey on 216 knowledge staff of four research institutes in Beijing. The results show that: knowledge staff have an overall low evaluation of the implementation status of total recognition rewards, among which they have a relatively high evaluation of work recognition, and a relatively low evaluation of compensation incentive and personal growth. The problems of total recognition rewards of knowledge staff are manifested in three aspects: firstly, the compensation does not match the performance, and lacks competitiveness in the industry; secondly, the performance appraisal is not scientific, the employees'' participation in decision-making is not enough, and the emotional communication between superiors and subordinates is not smooth; thirdly, the training effect is not ideal, the promotion mechanism is not perfect, and the honor incentive is not sufficient. In order to further optimize the incentive mechanism of knowledge staff, it proposes the following suggestions: the first is to establish a compensation system centered on value contribution, and carry out benchmarking management to enhance competitiveness and innovation capability; the second is to improve the performance appraisal system, strengthen the communication and feedback mechanism, and pay more attention to the emotional motivation; the third is to formulate a systematic training system, standardize promotion standards and procedures, and intensify the honor incentive mechanism.