In the presented study, a combined physiology, proteomics and gene expression study was performed using P. massoniana seedlings cultivated at various calcium levels. The aim of the study is to investigate the impacts of exogenous calcium on P. massoniana seedling growth and development and to reveal the underlying molecular mechanisms. The results showed that calcium deficiency lead to severe seedling growth and development inhibition while adequate exogenous calcium markedly improved the growth and development. The underlying mechanisms involved diverse calcium influenced biological processes and metabolism pathways including photosynthesis, carbohydrate metabolism and energy production, protein metabolism, secondary metabolism and calcium signal transduction and calcium ion homeostasis. In general, calcium deficiency inhibited or impaired these pathways and processes, while sufficient exogenous calcium improved and benefited these cellular events through regulating a number of related enzymes and proteins. Besides, adequate exogenous calcium supply relieved oxidation stress which occurred at low calcium level. Enhanced cell wall formation and consolidation and cell division also play a role in exogenous calcium improved P. massoniana seedling growth and development. Our study facilitates the elucidation of the potential regulatory role of calcium in P. massoniana physiology and biology and is of guiding significance in pinaceae plants forestry.