The effects of pre-hardening fertilization and autumn fertilization on seedling growth have been studied separately, but studies on their combined effects are relatively scarce. We studied the effects of pre-hardening fertilization type and autumn fertilization level on biomass allocation and root morphology of container-grown seedlings of Korean pine (Pinus koraiensis Sieb. et Zucc.), a valuable evergreen conifer distributed from Changbai Mountain to the Xiaoxing’an Mountains in northeastern China. Three pre-hardening fertilization types (conventional fertilization, exponential fertilization, and controlled-release fertilizer) were all applied with 72 mg of nitrogen. We also applied four nitrogen levels of autumn fertilization: 0 mg/plant, 2 mg/plant, 4 mg/plant, and 6 mg/plant. We found that autumn fertilization increased Korean pine seedling biomass accumulation and root growth by 65.91%–92.15% and 108.86%–141.48%, respectively. There was significant interaction between pre-hardening fertilization type and autumn fertilization level on biomass allocation and root morphology. Seedlings with conventional fertilization during the growing season have the best response to autumn fertilization, particularly in the 2 mg/seedling and 4 mg/seedling treatments. Autumn fertilization can be applied to the cultivation of high-quality Korean pine seedlings.