In order to clarify the effect of fulvic acid application on cotton in garlic-cotton intercropping production and realize high-yield, high-quality and high-efficiency fertilization of cotton, a two-season field experiment was conducted. The experiment consisted of no fertilization (CK), conventional fertilization (BF), conventional fertilization combined with low, medium and high rates of fulvic acid microbial agents (FA20, FA30, FA40), conventional fertilization combined with fulvic acid foliar fertilizer (BFL50), conventional fertilization combined with low amount of fulvic acid microbial agent and fulvic acid foliar fertilizer (FA20L50). The effects of different fulvic acid fertilizers combined with conventional fertilizers on yield, fiber quality and soil nutrients of cotton-garlic intercropping were studied. The results showed:(1) Compared with conventional fertilization, the yield of cotton lint increased with the increase of the fulvic acid microbial agents application rates. The average lint yield in FA30 and FA40 treatments increased significantly by 12.07% and 22.41% respectively in comparison with BF treatment. Meanwhile, FA30 and FA40 treatments significantly increased soil nitrate nitrogen, ammonium nitrogen and available potassium contents during seedling and full bloom, FA40 also increased soil available phosphorus contents. (2) The cotton lint yield of conventional fertilization combined with fulvic acid foliar fertilizer increased by 7.19% on average compared with conventional fertilization, and the SPAD of leaves increased by 7.78% during flowering stage, which significantly increased stomatal conductance and net photosynthetic rate, and decreased intercellular CO₂ concentration. (3) Compared with FA20 and BFL50, FA20L50 increased lint yield by 7.68%~27.51%, significantly increased fiber length, evenness index and breaking strength. Moreover, FA20L50 increased soil ammonium, nitrate, available phosphorus and available potassium contents. Soil phosphatase activity in FA20L50 was significantly higher than other treatments. The total amounts of nitrogen, phosphorus and potassium in cotton stems and leaves in FA20L50 treatment were significantly higher than other treatments, besides FA40 treatment. FA20L50 increased the total nutrient contents by 8.96%~47.35% in the bell shell in comparison with other treatments, and significantly improved the net photosynthetic rate compared with treatments without fulvic acid foliar fertilizer. In conclusion, conventional fertilizer combined with 300 kg/hm² fulvic acid microbial agent and 750 mL/hm² fulvic acid foliar fertilizer had the best application effect, which could improve the available nutrient supply of soil at all growth stages of cotton and facilitate the accumulation of nutrients in reproductive organs, thus promote the net photosynthetic rate of cotton leaves and improve the yield and quality of cotton.