The effects of silicon-doping on the microstructure of Al 0.07Ga0.93N/GaN multiple-quantum-well (MQW) have been studied by TEM. Significant changes of surface morphology and dislocation core structures have been observed due to Si-doping in the Al0.07Ga 0.93N barriers. Threading dislocations create surface pits in the MQW as a result of Si doping. With an increasing doping level, the pits change the shape from small faceted pyramid to large cone. The formation mechanism of the surface pits has been discussed from both dynamics and kinetics points of view. We have also observed nanopipes constrict to form closed core screw dislocations in the MQW due to Si-doping.