Based on computational fluid dynamic (CFD) and particle image velocimetry (PIV) technology, factor analysis method was used to study the effect of bottom clearance of flare on the flow characteristics of pumping system, and the occurred location change of submerges vortex and the submerged vortex core trajectory were analyzed emphatically. The results show that the occurred location of submerges vortex change along with the change of bottom clearance of flare, and the occurred location of submerges vortex along with the change of operating condition in the same bottom clearance of flare. With the decrease of bottom clearance, the velocity gradient varies greatly in the zone of the flare bottom. The bottom clearance h=0.8D was strongly suggested and the anti-submerged vortex device should be taken for this kind of box-type inlet passage. The velocity distribution contour of test section by PIV was similar to that by CFD, and the trajectory of submerged vortex by CFD was similar to that by PIV. It was also proved that the measured results showed great agreement with the calculated ones.