The theory of multi-skilled workers has been developed as multi-functionality theory (flexibility theory and flexible specialization theory) in Western countries and as skill formation theory (intellectual skill theory) in Japan. Multi-skill proficiency is a theory integrating these two perspectives and can be defined as the embodied ability of workers to perform intellectual and skilled tasks associated with integrated and comprehensive work. This study analyzed the impact of multi-skill proficiency on performance at the individual worker level, the moderating effect of flexible work methods, and the influence of competency-based human resource management on the formation of workers' multi-skill proficiency. Through empirical investigation and analysis, the following findings were revealed. Regarding the impact of multi-skill proficiency on performance, economic performance (productivity) showed higher significance than social performance (job satisfaction, organizational commitment). The interaction effect between multi-skill proficiency and flexible work methods on performance was not significant for social performance but was significant for economic performance. Among the six components of competency-based human resource management (competency-based HR management philosophy, cooperative labor-management relations, competency-based status management, competency-based compensation management, autonomous work management, and competency development management), competency-based HR management philosophy had the highest significance in its effect on multi-skill proficiency, followed by autonomous work management. As multi-skill proficiency thus influences the improvement of economic performance, managers should devote greater attention and effort to competency-based human resource management and flexible work methods for the development of workers' multi-skill proficiency.