Against the backdrop of accelerated digital and intelligent transformation, small and medium-sized retail enterprises are confronted with prominent contradictions in human resource management due to the industry characteristics of “scattered stores, frequent personnel turnover, and high labor costs”. This paper adopts a hybrid research method of “questionnaire + interview + multi-case analysis”, based on 296 valid questionnaires, in depth interviews with 23 stores and 12-month tracking data of 3 typical enterprises, systematically analyzes the current application status of digital tools and the bottleneck of efficiency transformation, and constructs a three in-one optimization strategy system of “precise empowerment by modules + full-process collaboration + efficiency transformation”. Empirical verification shows that this system can effectively solve core problems such as data silos and help enterprises improve the quality and efficiency of human resource management.