Tumor, like many other diseases, results from a complex interplay of genetic and environmental risk factors. In order to understand the mechanisms of underlying aetiology, we propose a novel framework for modeling Tumor Radiotherapy Mechanism (TRM) based on Gene-Environment Network (GEN) and Kinetic Theory of Active Particle (KTAP). In this method, the integrated TRM model is divided into four subsystems, each of which is composed of the active particles with different discrete states at molecular level. The kinetics of integrated TRM is dealt as the outcomes of complicated mutual interactions among active particles within different subsystems at molecular level, as well as external environment cofactors at systematic level. The simulations show that our method is efficient to illustrate a series of cellular activities during and after tumor radiotherapy, and it is very helpful to analyze the mechanisms of tumor cellular self-defensive, as well as the outcomes of tumor radiotherapy under different Ion Radiation (IR) strategies, via indicators of toxins, genome stability, and tumor cell mass etc.