This study aimed to investigate the effects of different functional fertilizers applied as seed soaking on cotton seed germination and salt-alkali tolerance, and to identify the optimal functional fertilizer for cotton cultivation in saline-alkali soils of Xinjiang. Two salt concentrations (0 and 50 mmol/L Na2SO4) were established, and four types of functional fertilizers, including peptide amino acids, fulvic acid, poly-γ-glutamic acid, and alginate oligosaccharides, along with seven combined formulations and a control group (CK), were tested. Seven traits, including germination potential, germination rate, germination index, fresh weight, dry weight, hypocotyl length, and root length, were measured. Correlation analysis, principal component analysis (PCA), and the membership function method were employed for comprehensive evaluation of salt tolerance. The results showed that: (1) compared with the non-salt treatments, the low-salt treatments increased average germination potential, germination rate, and germination index by 58.87%, 45.48%, and 43.08%, respectively. However, under low-salt conditions, fresh weight, hypocotyl length, and root length decreased by 39.00%, 57.22%, and 42.14%, respectively. (2) Compared with CK under non-salt conditions, treatment T9 (the combination of fulvic acid, poly-γ-glutamic acid, and alginate oligosaccharides) significantly increased germination potential, germination rate, and germination index (P<0.05), by 94.43%, 76.66%, and 84.75%, respectively. Treatment T7 significantly increased fresh weight, hypocotyl length, and root length (P<0.05), by 5.58%, 21.56%, and 4.46%, respectively, compared with CK. Under low-salt conditions, treatment ST8 significantly increased germination potential, germination rate, and germination index compared with SK (salt-stressed control), by 41.95%, 27.27%, and 29.09%, respectively. Treatment ST11 significantly increased fresh weight, hypocotyl length, and root length (P<0.05), by 6.99%, 42.74%, and 108.00%, respectively, compared with SK. (3) Correlation analysis indicated that germination rate was an important indicator for evaluating salt-alkali tolerance during germination. PCA transformed the seven traits into three independent comprehensive components, with a cumulative contribution rate of 81.668%. Based on the comprehensive salt-tolerance evaluation (D values), the treatments with the best salt tolerance during germination under non-salt and low-salt conditions were T9 and ST9, respectively. In conclusion, treatment T9, the combined formulation of fulvic acid, poly-γ-glutamic acid, and alginate oligosaccharides, was identified as the optimal formulation.