The invention provides a multi-station flexible clamping device and a multi-station flexible clamping method. The multi-station flexible clamping device comprises an upper-layer large turntable (10), small turntable power assemblies (20), a lower-layer small turntable (30), a motor flange (40) and a gear motor (50), wherein the upper-layer large turntable (10) realizes the transportation of clamped inner boxes, the small turntable power assemblies (20) realize the adjustment on the height and the angle of the lower-layer small turntable (30) at two positions, the lower-layer small turntable (30) realizes flexible clamping for the inner boxes, an the gear motor (50) drives the upper-layer large turntable (10) to rotate. With the adoption of the method, the accurate clamping mode in the case of no internal mode state of the inner boxes is provided, the complex line production of the box body processing becomes possible, the production efficiency is improved, meanwhile, the double-layer-turntable external drive mode is realized, and therefore, the device and the method have great significances for structure simplification and energy conservation and consumption reduction.