Glioma stem cells (GSCs) have been recognized as key players in glioma recurrence and therapeutic resistance, presenting a promising target for novel treatments. However, the limited understanding of the role GSCs play in the glioma hierarchy has drawn controversy and hindered research translation into therapies. Despite significant advances in our understanding of gene regulatory networks, the dynamics of these networks and their implications for glioma remain elusive. This study employs a systemic theoretical perspective to integrate empirical knowledge into a core endogenous network model for glioma, thereby elucidating its energy landscape through network dynamics computation. The model identifies two stable states corresponding to astrocytoma and oligodendroglioma, connected by a transitional state associated with GSCs, indicating the instability of GSCsin vivoand providing negative proof of their role as the cellular origin for glioma. We also obtained various stable states further indicative of glioma’s multicellular origins and uncovered a group of transition states that could potentially induce tumor heterogeneity and therapeutic resistance. This research proposes that the transitional states linking both glioma stable states are central to glioma heterogeneity and therapy resistance, suggesting a combination of apoptosis-inducing and differentiation-promoting therapies as a potential strategy. Our approach holds promise for advancing glioma therapy by providing a new lens through which to view the complex landscape of glioma biology.