Cotton root systems sustain photosynthesis by nutrient uptake and coordinate with above-ground growth to influence yield. This study explored the effects of fulvic acid (FA) and phosphorus (P) fertilizers on the relationships between cotton photosynthetic capacity (CAP) and root carbohydrate metabolism. A field experiment was conducted including five treatments: no P fertilizer (CK), 105 kg P2O5 ha-1 (P1), 150 kg P2O5 ha-1 (P2), 105 kg P2O5 ha-1 + FA (FP1), and 150 kg P2O5 ha-1 + FA (FP2). Results found that FP2 showed the most significant advantage, ensuring a suitable leaf area index (LAI) and cotton fractional interception of photosynthetically active radiation (IPAR) and consequently maintaining a high CAP. Compared with FP2, FP1 resulted in an increase in the boll loading of the root system (BLR) by 8.1% and the boll capacity of the root system (BCR) by 9.3%. From the peak flowering stage to the peak boll setting stage, sucrose and starch contents in FP1 were 6.2-19.2% and 26.5-27.9% lower than those in FP2, respectively. Conversely, fructose and glucose contents in FP1 were 6.4-10.8% and 7.2-8.8% higher than in FP2. The cotton reproductive organ biomass was increased by 11.1% and 14.7% relative to FP2. Moreover, FP1 achieved the highest yield, with an increase of 8.5% and 11.0% compared with P2 and FP2, respectively. Taken together, our study suggests that application of FP1 (105 kg P2O5 ha-1 + FA) could be a proper P fertilization method in cotton production of saline-alkali and arid regions.