Energy conservation dissipative particle dynamics (eDPD) is a mesoscale numerical simulation method of studying the heat transport process. In previous studies, when the Boussinesq assumption was introduced into the eDPD system to study the natural convection, the system was generally considered to be incompressible, and the effect of the thermal expansion of the eDPD system itself on the simulation results was often neglected, which would cause errors in the simulation. In the present study, the thermal expansion characteristic of the eDPD system is first investigated, and the thermal expansion coefficient βof the eDPD system is obtained by eDPD simulation. Then, based on the thermal expansion characteristic of the eDPD system itself, the natural convection is simulated with different values of Rayleigh number Raand different geometries, specifically, square cavity, concentric rings, and eccentric rings, and reasonable temperature and velocity fields are obtained, and they are in agreement with the simulated results by the finite volume method (FVM). The error between the eDPD simulation, in which the natural convection is driven by thermal expansion of the eDPD system itself, and FVM simulated result is considerably smaller than the errors observed in previous studies where Boussinesq assumption was directly adopted to simulate natural convection phenomena while neglecting the thermal expansion effect of eDPD system. It is shown that the effect of the eDPD system’s own thermal expansion characteristic needs to be considered when introducing the Boussinesq assumption in the eDPD system, and further, the calculation of the Ranumber is modified in this paper.