Molecular dynamics simulations are carried out to simulate thermal bubble nucleation processes in homogeneous and heterogeneous systems, respectively. It is found that the nucleation temperature of water confined in graphene nanochannels depends strongly on the channel height. Once the channel height is reduced below 3.1 nm, the nucleation temperature in the heterogeneous system is higher than that in the corresponding homogeneous systems, which violates the classical nucleation theory that homogeneous thermal bubble nucleation sets an upper limit for nucleation temperature under a given pressure. This abnormal phenomenon is attributed to the formation of a solid-like structure for the water confined in nanochannels, in which the whole water system has a lower potential energy than that in the corresponding homogeneous system. Decreasing or increasing the solid–liquid interaction strength may reduce or increase the nucleation temperature, which can explain the nucleation temperature’s dependence on surface properties in various heterogeneous systems. Meanwhile, we also observe the nucleation sites for different solid–liquid interfacial wettabilities. Based on this finding, it is demonstrated that the site of thermal bubble nucleation can be actively controlled by adjusting the solid–liquid interaction strength.