Nitrogen-polar (N-polar) wurtzite (WZ)-phase InGaN films suffer from severe zincblende (ZB)-phase inclusions and thus present a rough surface, which severely restricts its application in GaN-based optoelectronic devices. In this paper, several different pulsed modes were adopted to grow N-polar InGaN films with the purpose of suppressing the ZB-phase inclusions, and their effects on the surface morphology and crystal quality of the InGaN films were studied in detail. Our results demonstrate that the pulsed mode of continuously feeding In source while alternately injecting N and Ga sources can effectively suppress the formation of ZB-phase inclusions, due to the increased mobility of group-III adatoms on the N-polar surface. Benefiting from the suppression of the ZB-phase inclusions, the surface roughness of InGaN films is significantly reduced. Meanwhile, the screw dislocation density of the InGaN decreases from 1.4 × 109 to 6.0 × 108 cm−2. This work provides an approach to the growth of high-quality N-polar InGaN films free of ZB-phase inclusions for N-polar InGaN-based devices.