Root system plays a crucial role in plant growth and development by uptake of soil nutrients, which is affected by intensive use of NPK fertilizer. However, it is unknown how integrated nutrient management (INM) could affect the root growth and its nutrient uptake in the red soils of southern China. For this, the impacts of different INM practices on root morphological traits and root nutrient uptake were investigated in the pomelo tree. First, we investigated the spatial root distribution of various tree ages (i.e., 8, 13, 18, and 23 years old) and found the optimum root growth at 20–80 cm around the tree trunk in topsoil (0–20 cm). Hence, the pomelo trees were fertilized at 20–80 cm around the trunk, i.e., FFP (farmer fertilization practice), optimization NPK fertilizer (O) combined with lime (L) and mushroom residue (M) known as O+L+M treatment, and O+L combined with Mg fertilizer called as O+L+Mg treatment. We found that root length (RL) significantly increased by application of O+L+M (108.5 and 219.1 cm) and O+L+Mg (73.6, 66.8 cm) in topsoil and subsoil, respectively, in 2019. Similarly, root surface area (RSA) was significantly higher under INM, i.e., O+L+Mg > O+L+M > FFP. For root diameter (RD), O+L+M (0.8 mm) and O+L+Mg (1.5 mm) showed significantly lower diameter than FFP (2.54 mm). The root tips (RT) also improved considerably under INM practices compared with FFP. Besides, root nutrient contents (N, P, K, Ca, and Mg) also significantly improved under O+L+M and O+L+Mg over FFP. Similar trends of root growth and nutrients uptake were recorded in 2020. Overall, these findings suggest that INM plays a significant role in root development and nutrient uptake under acidic soil, which could be useful for maximizing crop productivity.