In order to study internal relation among the behavior of the weld pool, the microstructure of weld bead and the waveform of short-circuiting gas metal arc welding (S-GMAW), a high speed photograph-images analysis system was formed to extract characteristics of weld pool behavior. Three representative waveform control methods were used to provide partly and fully penetrated weld pools and beads. It was found that the behavior of the weld pool was related to the instantaneous power density of the liquid bridge at the break-up time. Weld pool oscillation was triggered by the explosion of the liquid bridge, the natural oscillation frequencies were derived by the continuous wavelet transform. The change of weld pool state caused the transition of oscillation mode, and it led to different nature oscillation frequencies between partial and full penetration. Slags flow pattern could be an indication of the weld pool flow. Compared with the scattered slags on fully penetrated weld pool, slag particles accumulated on partially penetrated weld pools. The oscillating promoted the convection of the welding pool and resulted in larger melting width and depth, the grain size, and the content of pro-eutectoid ferrite in the weld microstructure of S235JR increased, the content of acicular ferrite decreased.