Calcium (Ca) is an essential plant nutrient and cell signal element, but in the cultivation of container seedlings, the regulatory effect of Ca on seedling nitrogen nutrition and its regulatory mechanism have been neglected. Ectomycorrhizal fungi (ECMF) inoculation is widely used in forest container seedling cultivation. Thus, we added a certain amount of Ca to the culture matrix to determine how the cooperation between Ca and ECMF improves the nitrogen nutrition of Pinus massoniana ectomycorrhizal (ECM) container seedlings. We found that addition Ca significantly increased the relative abundance of Actinomycetota and Bacillota in the rhizosphere of ECM seedlings. These enriched bacteria cooperated with the ECMF and significantly enhanced extracellular enzyme NAG and LAP secretion. Meanwhile, adding Ca promoted the microbial nitrogen cycle in the ECM seedlings rhizosphere, and the relative abundances of nitrogen fixation genes (nifD, nifH, nifK) and the dissimilatory nitrate reduction gene (narH) significantly increased. In addition, Ca promoted the infection of ECMF on seedlings and induced the sprouting of absorptive roots with larger diameter (0.5 mm < RD ≤ 2.0 mm), i.e., ECM seedlings adopted a dual strategy of enhancing mycorrhizal symbiosis and improving root absorption area to obtain soil nitrogen. These effects contributed to an increase in microbial biomass nitrogen (MBN) and seedling nitrogen content by 20.65% and 54.38%, respectively. The results provide an effective method and theoretical reference for improving the quality of container seedlings and increasing the ECM plantations early productivity.