Amylopectin is an essential starch property, and the chain-length distribution of amylopectin (APCLD) is closely associated with the eating and cooking quality of rice. In this study, a series of recombinant inbred lines derived from an indica/japonicacross were planted in four areas with distinct ecological conditions (LN, SC, JS, and GD), and the relationship among APCLD, environmental factors, and genetic background was analyzed. The results showed that APCLD was strongly influenced by environmental factors, which dynamically changed from heading to the mature stage. The solar radiation, luminous flux, and light hours were positively correlated with Fa but negatively correlated with Fb1and Fb2. The temperature was negatively correlated with Fa and Fb1but positively correlated with Fb2and Fb3. The temperature was the primary factor affecting APCLD, followed by humidity and light. There was no significant correlation between the indicapedigree percentage and APCLD. Furthermore, we detected six quantitative trait loci related to Fa, Fb1, Fb2, and Fb3chains, several of which shared a similar region to previously reported loci, including DENSE AND ERECT PANICLE 1(DEP1). The truncated dep1allele increased Fa, Fb2, and Fb3but decreased Fb1in LN, whereas Fa was decreased but Fb1and Fb2were increased in JS. Elucidating the effects of climate factors and genetic background on APCLD could provide a theoretical basis and technical guidance for high-quality rice breeding.