Primary ramification morphogenesis has a significant influence on the yield of rapeseed. In order to quantify the relationship between rapeseed architecture indices and the organ biomass, a rapeseed primary ramification structural model based on biomass were presented. Intended to explain effects of cultivars and environmental conditions on rapeseed PR morphogenesis. The outdoor experiment with cultivars: Ningyou 18 (V1, conventional), Ningyou 16 (V2, conventional) and Ningza 19 (V3, hybrid), and designed treatment of cultivar-fertilizer, cultivar-fertilizer-density, and cultivar tests in 2011–2012 and 2012–2013. The experimental result showing that the leaf blade length of PR, leaf blade width of PR, leaf blade bowstring length of PR, PR length, and PR diameter from 2011 to 2012 were goodness, and their da values and RMSE values were −1.900 cm, 5.033 cm (n = 125); −0.055 cm, 3.233 cm (n = 117); 0.274 cm, 2.810 cm (n = 87); −0.720 cm, 3.272 cm (n = 90); 0.374 cm, 0.778 cm (n = 514); 0.137 cm, 1.193 cm (n = 514); 0.806 cm, 8.990 cm (n = 145); and −0.025 cm, 0.102 cm (n = 153), respectively. The correlations between observation and simulation in the morphological indices were significant at P < 0.001, but the dap values were <5 % for the second leaves length and the third leaves length, leaf blade bowstring length, PR length, and PR diameter, which indicated that the model’s accuracy was high. The models established in this paper had definite mechanism and interpretation, and the impact factors of N, the ratio of the leaf length to leaf dry weight of primary ramification (PRRLW), and the partitioning coefficient of leaf blade dry weight of primary ramification (PRCPLB) were presented, enabled to develop a link between the plant biomass and its morphogenesis. Thus, the rapeseed growth model and the rapeseed morphological model can be combined through organ biomass, which set a reference for the establishment of FSPMs of rapeseed.