The core employees are the key resources of gathering strength and innovating for scientific and technological small and micro enterprises (STSMEs). Aiming at the status quo of the education and training of core employees of STSMEs, as well as the solidification of the current incentive mechanism, the unreasonable salary system, the imperfect training mechanism and the lack of corporate culture, this study starts with the influence of core employees on STSMEs, and analyzes the problems existing in the education and training model and incentive mechanism of core employees of STSMEs. Combined with the characteristics of STSMEs, this study proposes specific measures to improve the incentive mechanism of core employees to stimulate the potentials of core employees, give full play to the value of core employees, and enhance the market competitiveness of STSMEs.