Silicon(Si)-doping was employed to improve the film quality of AlGaN/GaN heterostructure by radio frequency plasma-assisted molecular beam epitaxy. By Si doping during the buffer-layer growth, the electrical and structural characteristics of the films were improved. The electron mobility of the two-dimensional electron gas increases without changing the sheet carrier density. The full-width at half-maximums of (1012) X-ray rocking curves reduces. By the atomic force microscopy measurements, smooth surface morphology with micro-steps lower than unit cell height is found. We consider that the improvement of the film quality was caused by the reduction of the nano-pipes due to the growth-mode change into step-flow mode.