To explore the effects of different proportions of nitrogen substitute by organic fertilizer in total nitrogen input on banana growth and main quality can further reveal the correlation between different fertilizer supply modes and banana growth main quality, and provide theoretical support for finding the optimal ratio of nitrogen substitute by organic fertilizer. Banana continuous cropping experiment was conducted at the observation and monitoring site of Zhangzhou National Soil Quality Data Center in Fujian for consecutive years, no fertilizer was applied in the control (CK), while N 630 kg/hm² was applied in other treatments. Commercial organic fertilizer (MN) was used to replace inorganic fertilizer nitrogen (CN) in different proportions according to the percentage of organic fertilizer nitrogen in total nitrogen input, namely M0 (3/3 CN), M1 (2/3 CN+1/3 MN) and M2 (3/3 MN), then the effects of different MN substitution on banana growth and main quality were compared and analyzed. The results showed that:1) M0 and M1 maintained high growth potential, with shorter growth period and significantly higher yield than M2. The higher MN substitution significantly restricted the growth of banana plants and fruits. 2) MN substitution improved the storage quality and flavor quality of banana. The higher MN replacement, the faster banana color change rate and the longer the shelf life. At the same time, soluble sugar content of ripe banana fruit was increased, and the ratio of sugar to acid was increased significantly. 3) Soil nitrogen content was significantly correlated with the formation of banana flavor and quality. Soluble sugar content and sugar-acid ratio of the ripe banana fruits were extremely significantly or significantly negatively correlated with soil nitrate nitrogen and ammonium nitrogen contents. Banana titratable acid content and soil nitrate nitrogen content was significantly positively correlated. The higher available nitrogen content in soil, the lower banana sugar content, the higher soil acidity and the lower banana flavor quality. 4) Most volatile components in ripe banana fruits were esters, which accounted for 93.36%-98.66% of the total volatile components. M1 had the highest contents of 10 ester compounds, including isobutyl acetate, ethyl butyrate, ethyl isovalerate, isobutyl isobutyrate, 2-methyl propyl butyrate, isobutyl isovalerate. The ester and isoamyl isobutyrate were significantly higher in M1 than other treatments, while the content of isoamyl acetate and alcohol compounds was lower in M1. In summary, under the general level of soil basic fertility, especially when soil available nitrogen content was low, a large proportion of MN replacing CN could significantly limited the growth of bananas, reduced banana yield, but improved banana storage quality and flavor quality. Under the normal fertilization level, to maintain a higher banana yield and quality and a suitable growth cycle, 1/3 of organic fertilizer nitrogen input ratio is the better fertilization method.