Dalbergia odorifera T. Chen seedlings do not grow well in the typical red soils of tropical regions. Eighteen culture substances filled with different substrate combinations and proportions of red soil, coconut coir powder, deciduous leaf powder, and sand were used as to determine their effects on the growth, root system development, dry matter accumulation and allocation, leaf relative electrolyte leakage, chlorophyll content, root superoxide dismutase activity, root malondialdehyde content, and total soluble sugar content of D. odorifera. Results demonstrated that different substrate combinations and proportions had different effects on the performance of D. odorifera. All mixed substrates were better than any single substrate. The suitable substrate combinations and proportions of sand, coconut coir powder, and deciduous leaf powder mixed with red soil improved the growth, root architecture, and physiological characteristics of D. odorifera seedling. For example, groups C1-2 (coconut coir/red soil = 2/2, v/v, the same below) and C3-2 (red soil/sand = 2/2) exerted the best effects on plant growth and biomass accumulation. Groups C1-2, C2-2 (deciduous leaf powder/red soil = 2/2), and C3-2 remarkably enhanced root system development. Group C6 (coconut coir/red soil/sand = 1/1/1) substantially promoted root nodule development. Group C3-1 (red soil/sand = 3/1) exhibited the best effects on physiological characteristics. On the basis of the comprehensive evaluation of Euclid's multidimensional space mathematical model, we found that the suitable substrate combinations followed the order of C1-2 > C3-1 > C2-2. This research provides scientific guidance for the proper seedling culture of D. odorifera and the rational utilization of solid wastes such as coconut coir and deciduous leaves of Ficus elastica.