A two-stage filtration test system was successfully developed previously, and the objective of this study is to investigate the effect of pre-filter selection and face velocity of pre-stage and main-stage on the loading characteristics of a two-stage filtration system. Three different types of pre-stage filter media with different capture efficiency, i.e., G3, G4 and M5 pre-filters, were selected as filter type variables. Three different face velocities on pre-stage, i.e., 26.3, 45.0 and 65.2 cm.s(-1), and three different face velocities on main-stage, i.e., 2.1, 3.6, 5.2 cm.s(-1) were chosen as face velocity variables. Self-defined indexing parameters were used to analyze the effect of pre-filter in this study. The experimental results indicated that although M5 pre-filter with the highest capture efficiency presents the best protection to mitigate the pressure drop growth of main-filter, the pressure drop of M5 pre-filter itself increases the fastest, resulting in the shortest effective protecting time of M5 pre-filter in front of a main-stage filter, so the overall effectiveness of M5 pre-filter fades out due to the limited protection period. On the other hand, G4 pre-filter can run for a relative longer time while maintaining the pressure drop of the whole two-stage filtration system to increase relatively slowly. G4 pre-filter achieves highest T** value, outperforming the lowest efficient G3 pre-filter by its higher efficiency and the highest efficient M5 pre-filter by longer effective protection period. With the decrease of face velocity on either the pre-stage or the main-stage, the effectiveness of pre-filter on main-filter and the whole two-stage filtration system improves, by slowing down the pressure drop increasing rate of main-stage filter, which further contributes to extend the service lifetime of the main-filter and increase dust holding capacity of the whole filtration system. Besides, the specific resistance k(2) of the dust cake formed on main-filter were found deeply affected by the main-stage face velocity. With the face velocity on the main-stage increased, the specific cake resistance k(2) increased obviously, which implies that the dusts structure on the main-filter changed and became more compacted under higher main-stage filtration velocity. To better illustrate the relatively importance between pre-filter grade and filtration velocity selection, the analyzed performance indexing parameters were further arranged in a set of contour plots, which unveils the predominance of pre-filter grade over filtration velocity within the variation ranges tested in current study.