The scanning pentaprism system (PPS) is an effective method for guiding large flat optical processing, due to its advantages such as simple structure, high testing efficiency and precise measurement of low order aberrations. This paper established PPS′s mathematical model according to vectorial ray tracing theory, the analytical relationship between PPS′s performance and its components′ angular motion is obtained by least square fitting, which is useful for analyzing PPS′s sensitivity to components′ alignment errors. Afterward a fine alignment procedure is proposed. Experimental results show that PPS′s measurement error caused by alignment is better than 40 nrad after fine alignment. The result shows that PPS is practical for large flat testing.