[Objectives]  In this study, Chinese cordyceps at different stages of stroma initiation were used as the research materials to explore the changes in content of representative compounds and morphology of hyphae during the germination of Ophiocordyceps sinensis. [Methods]  Chinese cordyceps at three stages before germination (muscardine worm cadaver S1), early germination (mycelium breaking through the head of the worm S2) and after germination (forming stroma S3) were selected. The changes of the contents of polyphenols, polysaccharides, mannitol and urea were detected by ultraviolet chromatometry and adenosine by ultra-high performance liquid chromatography. The morphological differences of the hyphae in three stages were observed by scanning electron microscopy. [Results]  The morphological differences of the hyphae in the three stages during germination of Chinese cordyceps were significant. It was manifested that the hyphae began to fuse before germination (S1). After breaking through the head of the worm (S2) the hyphae were loose and slender. The hyphae are uniform in thickness and have micro warts on the surface after germination (S3). The content of polyphenols[(56.633± 2.312) mg/g ]and urea[(13.580±1.112) mg/g] was the highest in the S1 stage, which was significantly higher than that in the S2 and S3 stages(P<0.05), but the polysaccharide content was ( 22.045±1.341) mg/g lower than that in the S2 and S3 stages significantly(P<0.05). There no significant difference in content of polyphenols(39.608±2.145) mg/g, (37.365±1.972) mg/g and urea (1.892±0.345) mg/g, (2.322±0.423) mg/g between the stage of S2 and S3(P<0.05). The mannitol content in the S2 stage (42.099±2.986) mg/g was significantly higher than in S1 (33.660±3.473) mg/g and S3 (36.113±1.453) mg/g stages (P<0.05). The content of polysaccharide and mannitol in S1 lower than that S3 stages but the difference was not significant (P<0.05). The content of adenosine increased with the germination of stroma in Chinese cordyceps. [Conclusion]  The morphological changes of mycelium and the contents of representative compounds were significantly different before and after the germination of stroma in Chinese cordyceps.