Salt stress is the main factor restricting the growth and grain yield of wheat grown in salinized soils. The potential of traditional agricultural technologies will be explored to increase outputs in such conditions. In addition, increased amounts of organic fertilizers are also used to alleviate the effects of salt stress. Together, traditional technologies and fertilizer applications could make up a technical application system integrating traditional and modern agriculture. Understanding the mechanism of salt resistance in wheat is important for wheat production. The concentrations and balance of endogenous hormones are closely linked to growth and development in wheat. However, little is known about the relationship between endogenous hormones and salt resistance, and the effects of organic fertilizer on these factors, in wheat under salt stress. The objective of this research, therefore, was to determine the concentrations and balance of endogenous hormones under salt stress in a salt-resistant cultivar of wheat (Triticum aestivum L. Yumai49-198). The results will help to elucidate the mechanism of salt resistance and provide valuable information to alleviate the negative effects of salt on wheat by optimizing the amount of organic fertilizer. First, we examined the difference in salt tolerance of wheat seedlings grown with various amounts of organic fertilizer and various concentrations of salt. From these results, we determined the appropriate amounts of fertilizer and salt for further investigations. We then used a pot experiment to analyze the changes in endogenous hormone contents in seedlings grown in increasingly saline soils. Application of organic fertilizer markedly alleviated the inhibitory effect of salt on wheat seedlings treated with 150 mmol/L NaCl, but had no effect when the NaCl concentration was 450 mmol/L. Fertilizer was most effective at an application rate of 25000 kg/hm² and ineffective at 45000 kg/hm² or higher. Furthermore, when wheat seedlings were treated with 150 mmol/L NaCl in combination with 0 (CK), OF-15000 (15000 kg/hm², low level), OF-25000 (25000 kg/hm², medium level) and OF-35000 (35000 kg/hm², high level) for 8 d, soil salinity increased with increasing amounts of organic fertilizer. Compared with the control, seedlings treated with organic fertilizer showed lower abscisic acid (ABA) content under salt stress, and this decreased level of ABA was an important factor in salt tolerance. In addition, seedlings in the organic fertilizer treatments showed markedly increased contents of auxin (IAA) and gibberellin (GAs), suggesting that under salt stress, the salt-resistant wheat seedlings had greater ability to synthesize IAA and GAs, which was beneficial for seedling growth. In the three organic fertilizer treatments, the zeatin riboside (ZR) contents increased in shoots and decreased in roots as salt stress increased, compared with their respective contents in the control (no fertilizer). This result suggested that salt stress stimulated the translocation of ZR from the root to the shoot to maintain seedling growth in the salinized environment. The ratios of IAA/ABA, GAs/ABA, and ZR/ABA also increased in salt-resistant seedlings under salt stress. Based on the above results, it appears that seedlings showing increased salt resistance in the organic fertilizer treatments were better able to regulate endogenous hormone contents to adapt to salt stress. Therefore, their growth was less inhibited than that of seedlings in the control (no fertilizer) under salt stress.