AbstractThis study aims to explore the formation mechanism of starch structure and the relationships between the appearance quality and starch structure of soft rice under different nitrogen levels. We comprehensively investigated the physiological aspects, starch structure variations, and appearance quality of soft rice in response to different nitrogen applications. The results showed that under the moderate nitrogen application (270 N), the soft rice exhibited the highest AGPase activity, the highest large‐starch granule content, and the lowest chalkiness. Under the highest nitrogen application (360 N), the soft rice exhibited the highest GBSS and DBE activity and the lowest SBE activity, the highest content of long‐branched amylopectin, the lowest relative crystallinity, the fewest ordered structures, the most amorphous structures, the largest semi‐crystalline lamellar thicknesses, and the highest transparency of chalk‐free rice. In conclusion, moderate nitrogen fertilization (270 N) improved the AGPase activity, which leaded to fuller starch granules and more compact endosperm in soft rice. Thus, the grain chalkiness of soft rice decreased. Continuous nitrogen application (0‐360 N) constantly increased the GBSS and DBE activity and reduced the SBE activity in soft rice, leading a lower content of short‐branched amylopectin and a higher content of long‐branched amylopectin in soft rice. Thus, the relative crystallinity and ordered structures of soft rice were reduced. These structures improved the transparency phenotype of soft rice.