Abstract: In this study five periods were chosen as the observation points during germination and the increment change of the seed of Masson pine (Pinus massoniana) of each period were measured. Meanwhile, The GC-MS, HPLC-MSn and Li-6400 CO2 were used to analyze the contents of fatty acids, the compositions of proteomics and the photosynthesis rate of the seeds respectively during the germination. The results showed that the contents of fatty acid and starch were the highest in the first two periods. During the germination stage, the fat and starch were transformed to small molecular substances to supply the development of root and bud, and the value reduced to 0 at seeding stage. The results of SDS-PAGE showed that the positions of the protein bands were unchanged but only the abundances of the protein were reduced. The high molecular band was emerged during budding, and the molecular weight was reached 52.0 kDa in seedling stage. Significant difference protein spots in maturity and seedling were analyzed, they were storage protein-cones protein and the key enzyme of photosynthesis -Rubisco, which indicated that the new functional protein was formed to regulate the growth with the storage protein degrading. Because of a high content of fat in Masson pine, the storage fat and protein were mobilized to supply energy and raw material in early growth stage of Masson pine. The material metabolism was very vigorous, especially while the radicle broke through the seed coat. At last, during the germination stage, the Masson pine seed underwent the process from heterotrophic to autotrophic, and this stage was predicated as the turning point according to the appearing of Rubisco and the compensation point of CO2.