Phonon heat transport in thin films is solved by using dissipative particle dynamics with energy conserving (eDPD), and the size effect on thermal conductivity is analyzed. When the thickness of a film is comparable with the phonon mean free path, boundary scattering becomes dominant. To incorporate both the phonon phonon scattering effect and phonon-boundary scattering effect, we adopt a particle particle collision flux model and a particle wall collision flux model in eDPD. Using these models, we investigated the heat transport between two parallel and infinite plates for 0.1 < Kn < 10 where the heat transport is both ballistic and diffusive. The temperature jump is observed at the boundaries and the temperature profiles are in good agreement with the solution to the equation of phonon radiative transport (EPRT). Moreover, we vary the thickness of the film and calculate the corresponding effective thermal conductivity to investigate the size influence. The present results are compared with the simple analytical solution based on Matthiessen's rule and the effective thermal conductivity equation derived from the EPRT and it is found that the effective thermal conductivity can be predicted correctly by eDPD. (C) 2016 Elsevier Ltd. All rights reserved.