A field random plot experiment was carried out on yellow-brown soil to study the effects of 4 fertilization methods including no fertilization, inorganic fertilization, organic - inorganic fertilization and straw return with inorganic fertilization on soil profile quality and crop yield. The results showed that after 13years of continuous fertilization, the contents of soil organic matter (SOM), total nitrogen (TN), alkali-hydrolyzed nitrogen (AN), total phosphorus (TP), available phosphorus (AP) and available potassium (AK) under different fertilization treatments decreased with increasing of soil depth. Long-term application of inorganic fertilizer acidified the soil, while combined application of organic and inorganic fertilizers effectively alleviated soil acidification. Compared with no fertilization treatment, inorganic fertilization treatment only had a significant effect on nutrient contents in topsoil layer (0-20 cm), while organic-inorganic fertilization and straw return with inorganic fertilization treatments significantly increased nutrient contents in 0-40 cm soil layer. Compared with inorganic fertilization treatment, TN content in 0-40 cm soil layer under organic-inorganic fertilization and straw return with inorganic fertilization treatments increased by 11.2% and 22.3%, respectively. In 0-20 cm soil layer, the contents of SOM, TP and AP under of organic-inorganic fertilization and straw-return with inorganic fertilization treatments were higher than those under inorganic fertilization treatment, and the contents of SOM and AK under straw return with inorganic fertilization treatment were higher than those under inorganic fertilization treatment in whole soil profile, which indicates that long-term straw return can promote the migration and accumulation of nutrients to deeper soil layers. Moreover, long-term fertilization significantly enhanced wheat yield, but no difference was found among inorganic fertilization, organic-inorganic fertilization and straw return with inorganic fertilization treatments. The straw return with inorganic fertilization treatment reached the greatest improvement in soil quality index (SQI) and crop yield, with straw return increased SQI by 14.9% and sweet potato yield by 39% compared to inorganic fertilization. SQI of above 60 cm layer under long-term fertilization had significant positive correlation with annual crop yield, indicating that the effect of soil profile nutrients on crop growth should not be neglected. In conclusion, compared to inorganic and organic-inorganic fertilization, return straw with inorganic fertilization has the best effect on fertilizing soil and increasing crop yield under the sweet potato and wheat rotation system.