As an important force in China's economic life, the importance of small and medium-sized enterprises(SMEs) is increasingly prominent. In the fierce market competition, whether SMEs can obtain competitive advantage depends on the efficiency of human resource management to a great extent. Due to the constraints of objective conditions, the efficiency of human resource management in SMEs is still insufficient, and the implementation of human resource management benefit audit provides a feasible way to improve the efficiency of human resource management in SMEs. Taking this as the research object, this paper deeply analyzes the main problems in the implementation of human resource management benefit audit in SMEs from the aspects of theoretical basis, practical tools and external environment, and puts forward countermeasures and suggestions to effectively solve the above problems, so as to provide useful reference and Enlightenment for the effective implementation of human resource management benefit audit in SMEs.