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In order to reveal the interaction between biochar and nitrogen on affecting the root morphology and system architecture of cotton during fullbloom stage, the root systems and root growth angles of cotton by layered digging at 0~10cm soil layers and below were analyzed through the generalized additive model and redundancy analysis under different biochar application regimes(N0(conventional nitrogen application, 0.3t/hm2), N0+ Bc1%(N0+ 1% cotton biochar as quality of topsoil), Nl+ Bc1%(0.21t/hm2+ 1% cotton biochar as quality of topsoil), Nl+ Bc2%(0.21t/hm2+2% cotton biochar as quality of topsoil)and N0+Bc4%(N0+4% cotton biochar as quality of topsoil). The results showed that there was no significant difference between Nl+Bc2% and N0+Bc1% in average fine root length, but it was significantly higher than those of N0+bc4%, Nl+Bc1% and N0(p<0.05). The average root branch angle was 83°17′ at 0~10cm soil layers and it showed no significance between each group(p>0.05), however, root branching angle was significantly larger at deeper soil, and root branching angle was 101°48′ under Nl+Bc2%. Biochar application changed the cotton root spacing section(p<0.001), and it was more significantly changed in direction with water coming of 270°, where the longest was 4cm under N0+Bc4%. The specific root length density of cotton was altered by biochar application regimes(p<0.02)and soil depth(p<0.001)separately. The redundancy analysis showed that the main factors influencing the root length density were the vertical angle of fine and medium roots in the topsoil, the vertical angle of fine root in the bottom and the percentages of very fine root length. Among root traits, the fine root length was most closely related to vertical root angle. This suggested that vertical root distribution constitutively affected fine root length. Significant genotypic variation existed in the root diameter and root growth angle in interaction with biochar and nitrogen. To sum up, the application of 0.21t/hm2 nitrogen with biochar of 1%~2% topsoil mass mainly changed the root system architecture and morphology of cotton at the bottom soil(>10cm)and 2% biochar made up for the negative effect of nitrogen deficiency.