To promote the innovative reform of physical education teaching, this paper adopts the multivariate statistical analysis method to construct a set of multivariate evaluation system. A comprehensive assessment and classification of teaching quality was realized through principal component analysis, flower-pollinated cluster analysis and robust factor analysis model. The teaching quality assessment system of the physical education option course designed in this study includes four primary indicators and 13 secondary indicators. The results showed significant differences in teaching quality among teachers, and the three retained principal factors could reflect 78.15241% of the student performance information, which provided a vital quality control reference for physical education teaching.