Improving the biomass and nutritional quality of Brassica napus is important for its breeding and resource conservation, but there are few studies on the effects of high altitude on its biomass and quality. In this study, 27 varieties of Brassica napus were cultivated both at 1600 m and 150 m altitudes to investigate the effect of different altitudes in the biomass and quality traits of B. napus. At high altitude, all B. napus varieties exhibited decreased picking period, reduced fresh and dry weights, diminished stem length and diameter, as well as lowered nitrogen (N), phosphorus (P), and kalium (K) contents. The soluble sugar and cellulose contents of some varieties decreased, while ascorbic acid and protein increased by 74% and 85%, respectively. Furthermore, histology microscopical observation showed cell size increased and cell density decreased in the shoot apical meristem (SAM) after bolting and at high altitude, compared to those cells before bolting and at low altitude. Transcriptome analysis showed that sucrose phosphate synthase (SPS), sucrose synthase (SUS), fructose‐1,6‐bisphosphate aldolase (FBA1), and alpha‐galactosidase (AGAL2) genes were significantly up‐regulated during the after‐bolting period at different altitude. This study will be helpful to further understand the influence of high altitude ecosystem on biomass and quality for Brassica napus resource and evolution.