Near-natural transformation can convert artificial monoculture forests into mixed forests with diverse ages, multi-layered structures, and enhanced ecological functions. This transformation optimizes stand structure, improves soil physical and chemical properties, and enhances stand productivity and species diversity. This study aimed to explore the relationship between the underground roots and aboveground growth of Pinus tabuliformis and Populus tomentosa under conditions of nutrient heterogeneity, with the goal of advancing plantation transformation. This research focused on 1-year-old Populus tomentosa and 5-year-old Pinus tabuliformis, employing two planting densities (25 cm and 50 cm) and three fertilization levels, low (50 g·m−2), medium (100 g·m−2), and high (200 g·m−2), using Stanley Potassium sulfate complex fertilizer (N:P:K = 15:15:15). Each treatment had three replicates, resulting in a total of nine experimental groups, all planted in circular plots with a radius of 1 m. Standard major axis (SMA) regression was used to analyze the allometric relationship between underground fine root biomass and aboveground organ biomass. This study further explored correlations between fine root length, root surface area, volume, biomass, and aboveground biomass, culminating in a mixed-effects model. The mixed-effects model quantified the relationships between underground roots and aboveground growth in varying soil nutrient environments. The results indicated optimal root growth in Populus tomentosa and Pinus tabuliformis, characterized by maximum root length, surface area, and volume, under conditions of 200 g·m−2 soil nutrient concentration and 50 cm planting distance; Populus tomentosa fine roots had a vertical center at a depth of 8.5 cm, whereas Pinus tabuliformis roots were centered at depths of 5–7.5 cm, indicating differing competitive strategies. Pinus tabuliformis exhibited competitive superiority in the soil’s surface layer, in contrast to Populus tomentosa, which thrived in deeper layers. The study of the allometric growth model revealed that under conditions where the nutrient gradient was 200 g·m−2 and the planting distance was 25 cm, Populus tomentosa demonstrated its highest allometric growth index (2.801), indicative of positive allometric growth. Furthermore, there was a notable inclination of resource allocation towards the aboveground, which enhances the accumulation of aboveground biomass. The mixed-effects model equation showed a clear linear relationship between underground roots and aboveground biomass. The final fitting coefficient of the model was high, providing a robust theoretical basis for future management practices. The mixed-effects model revealed the following hierarchy of fixed-effect coefficients for root system characteristics affecting aboveground biomass: fine root volume (132.11) > fine root biomass (6.462) > root surface area (−4.053) > fine root length (0.201). In subsequent plantation reconstruction and forest management, increasing soil fertility and planting distance can promote the growth of underground roots and biomass accumulation. Appropriately increasing soil fertility and reducing planting distance can effectively promote aboveground biomass accumulation, achieving sustainable forest development.