Abstract: The development of new sweet potato varieties with high starch and anthocyanin contents in storage roots has been the key objective of sweet potato research. In this study, natural variations in five white-fleshed sweet potato (with white or pale yellow flesh color) varieties (lines) and five purple-fleshed sweet potato (with purple flesh color) varieties (lines) were analyzed for the effects of environments on quality traits of storage roots in 2012 and 2013. Analyses of variance and correlation were conducted for the two types of sweet potato accessions in six regions of Chongqing City. The results showed significant differences (P < 0.05) or extremely significant differences (P < 0.01) in yield-related traits (e.g., fresh yield, starch yield and dry root yield) and quality traits (e.g., starch content, dry matter content and anthocyanin content) among genotypes and environments. For all the tested sweet potato varieties (lines), genotypic effect on starch content was greater than environmental and temporal effects. For white-fleshed sweet potato accessions, environmental effect on yield-related traits was greater than genotypic and temporal effects. For purple-fleshed sweet potato, however, environmental and temporal effects on yield were greater than genotypic effect. While higher yield was obtained at intermediate altitude (i.e., Wanzhou or Youyang) conditions, better palatability was obtained at low altitude (i.e., Hechuan and Beibei) conditions. Furthermore, the grade of palatability at intermediate altitude was higher than that at high altitude (i.e., Qianjiang or Wuxi) conditions. The mean variation coefficients (CV) of morphological traits (e.g., stem diameter, vine length and breach number, CV = 0.30) and yield-related traits (CV = 0.28) were high, those of quality traits (e.g., dry matter content, starch content and palatability) was even much smaller (CV = 0.11), while that of anthocyanin content was also high (CV = 0.28). Correlation analysis suggested extremely positive correlations (r ≥ 0.700) among fresh yield, starch yield and dry root yield of sweet potato. Starch content had extremely positive correlations with dry root yield and starch yield (r ≥ 0.363). For white-fleshed sweet potato accessions, stem diameter had extremely significantly positive correlation with vine length (r = 0.439), extremely significantly negative correlation with starch content (r = 0.433), and significantly negative correlation with starch yield (r = 0.318). For purple-fleshed sweet potato accessions, commodity rate was significantly positively correlated with branch number, starch yield and dry root yield (r = 0.345, 0.368 and 0.357, respectively). In addition, a significantly negative correlation (r = 0.397) was noted between vine length and branch number. It was concluded that affecting factors of yield, quality and agronomic traits of different genotypic accessions of sweet potato were different. Individualized selection and breeding approaches should be adopted on the basis of sweet potato types and breeding targets. The results provided valuable theoretical reference for screening advantageous environmental factors for quality traits formation, improvement of breeding approaches, and cultivation techniques of sweet potato. This could facilitate the promotion of quality improvement of sweet potato.