Understanding the characteristics of partially premixed flames (PPFs) under transcritical conditions is of critical importance for the development of fuel-rich staged rocket engines. While substantial progress has been achieved for transcritical non-premixed flames (NPFs), comparatively little effort has been made to investigate transcritical PPFs. To this end, a series of transcritical counterflow gaseous hydrogen/liquid oxygen (GH2/LOX) PPFs is simulated to investigate the thermodynamic structure of PPF and to examine the effects of molecular diffusion modeling, strain rate, and the equivalence ratio at the fuel-rich side on PPFs in physical space and mixture fraction space, as well as reduced temperature/reduced pressure space. The comparisons between the NPF and PPF demonstrate that the PPF exhibits a bimodal structure in physical space: a premixed reaction zone at the fuel inlet side and a non-premixed reaction zone at the oxidizer side. In mixture fraction space, the C-shaped structure of PPF is observed owing to the differential diffusion of species. It is found that the choice of molecular diffusion model has a significant impact on PPF structure. The presence of a loop at subcritical pressures in a reduced temperature/reduced pressure space is caused by the differential diffusion of species and the formation of [Formula: see text] in the non-premixed reaction zone. Furthermore, the results indicate that the premixed reaction zones in the PPFs are very sensitive to the change in strain rate and/or equivalence ratio of the premixed mixture at the fuel inlet side. For a given equivalence ratio, increasing strain rate can suppress the differential diffusion effect and the C-shaped structure, while it has a negligible impact on the non-premixed reaction and hence on loop formation.