Seasonal drought and summer soil high-temperature stress in Southern China often lead to decreased yield and quality of Annona squamosa. It is important to explore reasonable and effective water and fertilizer management measures as well as cover measures to improve the soil hydrothermal conditions in orchards to realize the increase in yield and quality of Annona squamosa. This study involved a two-year (2022–2023) field experiment in Yun County, Lincang City, Yunnan Province, using three factors and a three-level orthogonal test, resulting in nine different experimental treatments for water, fertilizer and heat. The three irrigation levels were W1 (soil moisture content of 55% of field moisture capacity), W2 (soil moisture content of 75% of field moisture capacity) and W3 (soil moisture content of 85% of field moisture capacity). The three fertilizer levels were F1 (1666 kg·hm−2), F2 (2083 kg·hm−2) and F3 (2500 kg·hm−2), and the three cover methods were A1 (no cover), A2 (fresh grass cover) and A3 (straw cover). The effects of these treatments on soil hydrothermal conditions, growth indices and fruit yield and quality of Annona s1uamosa were systematically monitored and analyzed, and the relationships between these treatments and yield and quality was analyzed based on a Mantel test. The results showed that T5 (W2F2A3) had the highest average soil moisture content over two years, followed by T7 (W3F1A3). The T7 (W3F1A3) treatment effectively reduced soil temperature by 5 °C compared to T1 (W1F1A1). T5 (W2F2A3) had the highest average yield over two years, with an increase of 33.99% compared to T1 (W1F1A1). Additionally, T5 (W2F2A3) has the highest average soluble solids, soluble sugars and vitamin C content over two years, with increases of 28.13%, 13.36% and 4.86%, respectively, compared to T1 (W1F1A1). A Pearson correlation analysis showed that there was a significant correlation between Annona squamosa growth and soil moisture content and soil temperature, and the Mantel test showed that soil hydrothermal conditions had significant influence on the growth and yield. T5 (W2F2A3) has the highest comprehensive benefit in promoting growth, increasing yield and improving quality for the plant. The effects of different irrigation quantities, fertilizer amounts and different cover measures on the coupling interaction for soil hydrothermal status in the root zone, growth, yield and quality of Annona squamosa were investigated, providing reliable theoretical support for the scientific planting model of Annona squamosa in the low-heat river valley of Yunnan Province.