We used canonical correlation analysis in this study for four agronomical traits including yield traits, the main stem traits, branching characteristics and pod traits of Brassica juncea species from 113 germplasms. The results showed that 1) Among the 18 traits investigated in the present study, the average value for Tibetan B. juncea species is 1.88 folds of that from the species in the adjacent provinces, and the population coefficient of variation is 10.22% and higher than that of the adjacent regions; 2) In the Tibetan B. juncea species, yield per plant is prominently dependent on pods per plant and 1000-grain weight. However, yield per plant of B. juncea in the neighboring provinces is mainly determined by efficient pods per plant. In the neighboring countries, the dominant factors are efficient pods per plant and 1000-grain weight. 3) The yield traits in Tibetan B. juncea are mainly attributed to pod traits, followed by branching characteristics and main stem traits. In terms of the species from adjacent regions, the most important yield-determining factor is main stem traits, followed by the branching characteristics and pod traits. 4) Among the 4 sets of traits analyzed, there are 9, 8 and 5 pairs with significant or extremely significant correlation in the species from Tibet, the adjacent provinces, and the neighboring countries respectively. The Tibetan B. juncea species exhibited close relevance as well as gradient differences in the agronomical traits with that of the species from the adjacent provinces and countries.