To reduce the analysis error for highly subjective scoring and unilateral evaluation in traditional failure mode and effects analysis (FMEA) for machine tools, a modified FMEA is presented based on set pair analysis (SPA) to which two indicators called M and R are added. In this process, risk priority number (RPN) can be calculated through the connection degree of SPA after the failure mode and evaluation indicator of each mode have been determined. Finally, the most serious failure mode can be determined. Taking a tool magazine and automatic tool changer (ATC) as an example, the feasibility of the proposed FMEA is demonstrated.