Masson pine (Pinus massoniana) is primarily present in southwest of China, which are severely deficient in inorganic phosphate (Pi). Although some studies identified transcriptomic and proteomic responses to Pi deficiency in Masson pine seedlings, miRNAs and molecular responses in different tissues have not been well studied. To shed further light on the complex responses of Masson pine to Pi deficiency, a spatiotemporal experiment was performed to identify differentially expressed mRNAs and miRNAs under Pi deficiency. Spatiotemporal analyses of 72 RNA sequencing libraries provided a comprehensive overview of the dynamic responses of Masson pine to low-Pi stress. Differentially expressed gene analysis revealed several high-affinity phosphate transporter genes (PHT1-1, PHT1-4, PHT1-5 and PHT1-12) and a nitrate transporter gene (NRT), reflecting the crosstalk between nitrate and Pi homeostasis in plants. miRNA differential expression analysis identified several families that were associated with Pi deficiency, such as miR399. In addition, some other families were dramatically changed in response to Pi starvation, such as miR156, miR169, and some novel miRNAs. Integrated analysis of DE miRNAs and mRNAs indicated that “amino acid metabolism”, “energy metabolism” and “lipid metabolism” were most enriched under Pi deficiency. This study provided essential regulation information between miRNAs and target genes on the response of Masson pine seedlings to Pi deficiency, which will aid in further elucidation of the biological regulatory mechanisms of pines in response to low-Pi stress.