This paper carries on an empirical analysis on compensation difference in public service units by sampling methods. And the result of regression model shows that the characteristics of labor force, such as gender, education, tenure, position, have significant influences on compensation difference, especially education and position factors more remarkable. But the compensation difference is comparatively unconspicuous in public service units, variables excluded in this model has a greater proportion. This result indicates that there still are unreasonable factors in compensation structure of public service units, and motivation factors are comparatively deficient.