The complex interaction between exothermic processes and flow-field is numerically simulated for a hydrogen-air premixed pulsed jet combustion system (PJC). The results show that the flames propagating in the sub-chamber are wrinkled due to strong baroclinic effect. The total momentum of pulsed jet through the orifice oscillates quasi-periodically because weak shock waves travel between the top and bottom walls of the sub-chamber. Such oscillation of injected jet forms the basic shape of wrinkled flame front. This wrinkled flame front generates vorticity due to baroclinic effect, then the induced vortices stretch the flame front to cause local quenching (negative OH production), which in turn generates pressure waves travelling normal to the flame front. Therefore, the flame front propagating in the main-chamber is subjected to the self-deformation mechanism due to baroclinic effect, even if the basic shape of flame front is determined by the injected jet, i.e. by the Kelvin-Helmholtz instability.