In view of the dual characteristics of "automation" and "destructiveness" of the automatic hardness testing system, this paper systematically expounds the particularity of its measurement system analysis (MSA), and points out the limitations of the traditional Gauge Repeatability and reproducibility (GR&R) method in the identification of variation sources and experimental design. On this basis, a "process decoupling hybrid GR&R" experimental strategy is proposed, which decouples the hardness testing process into two sub processes: indentation generation (destructive) and indentation measurement (non-destructive). Nested design and cross design are used to separate and quantify the variation sources, respectively. Through the construction of double detection unit automation platform, the systematic MSA experiment was carried out, and the analysis of variance was used to evaluate the influence of equipment repeatability, reproducibility and interaction. The results show that the proposed method can effectively identify the dominant variation sources, and provide a feasible analysis framework for the performance evaluation and optimization of the hardness automatic testing system, which has strong engineering applicability and popularization value.