Background: Chinese hickory ( Carya cathayensis ) and pecan ( C. illinoinensis ) are popular nut trees with high economic value in the family Juglandaceae, due to the richness in nutrients and multiple health factors in their nut kernels. However, the considerable in-situ germination of the nut seeds severely impact the quality of the kernels. The fundamental meta bolic mechanism of in-situ germination has been widely reported in major crops but rare in nut crops. Results: We sampled non- and pre-sprouted Chinese hickory nut kernels and performed liquid chromatography-tandem mass spectrometry (LC–MS/MS)-based metabolomic analyses. Comparative metabolomic analyses revealed 35 6 significantly-changed metabolites during in-situ germination. Detailed analysis emphasized the increasing accumulation and dynamic changes in compounds of primary mechanism and energy supply for in-situ germination. The results highlighted the importance of allocation shift and accumulation on four classes of primary metabolites and their derivatives, and two secondary metabolite classes between the transitions of germination initiation and germination and seedling establishment during the process. Metabolites related to carbohydrates and nitrogen metabolism, and few harmful to human health also demonstrated increasing accumulation along the process. Conclusions: The findings flourish our understanding of the metabolic mechanisms of in-situ germination and will be useful for future application in molecular breeding in Chinese hickory.