Desert soil is one of the most severe conditions which negatively affect the environment and crop growth production in arid land. The application of organic amendments with inorganic fertilizers is an economically viable and environmentally comprehensive method to develop sustainable agriculture. The aim of this study was to assess whether milk tea waste (TW) amendment combined with chemical fertilizer (F) application can be used to improve the biochemical properties of sandy soil and wheat growth. The treatments included control without amendment (T1), chemical fertilizers (T2), TW 2.5% + F (T3), TW 5% + F (T4) and TW 10% + F (T5). The results showed that the highest chlorophyll (a and b) and carotenoids, shoot and root dry biomass, and leaf area index (LAI) were significantly (p < 0.05) improved with all amendment treatments. However, the highest root total length, root surface area, root volume and diameter were recorded for T4 among all treatments. The greater uptake of N, P, and K contents for T4 increased for the shoot by 68.9, 58.3, and 57.1%, and for the root by 65.7, 34.3, and 47.4% compared to the control, respectively. Compared with the control, T5 treatment decreased the soil pH significantly (p < 0.05) and increased soil enzyme activities such as urease (95.2%), β-glucosidase (81.6%) and dehydrogenase (97.2%), followed by T4, T3, and T2. Our findings suggested that the integrated use of milk tea waste and chemical fertilizers is a suitable amendment method for improving the growth and soil fertility status of sandy soils.