A transient model of a Capillary Pumped Loop (CPL) is proposed to predict the thermal and dynamic behavior, which includes two coupled modules: the thermal model and the hydrodynamic module. The thermal module is based on the nodal method and the dynamic module of the liquidvapor interface is based on the molecular kinetic theory. Especially, a thermal non-equilibrium model is proposed to predict the temperature of evaporator, which is unlike some traditional numerical method associate with the CPL system. In the present model, vapor is treated as a compressible phase, so an equation of state (EOS) should be used to complete the controlling equations. A mesoscaled multiphase lattice Boltzmann model (LBM) is proposed to analyze the different working fluids, which can help us to choose appropriate EOS. Combining these two models for different scale, the behavior of ammonia is analyzed by the LBM. The processes such as the start-up, the temperature oscillations in the reservoir and the heat load change in the evaporator are investigated by the transient model of a whole CPL. The numerical results of the LBM show that the PengRobinson (P-R) equation is more appropriate for the ammonia and the results of the macroscopic transient model show that why the start-up of a CPL becomes a failure easily and temperature oscillations in the reservoir are disadvantageous to the operation of CPL. With this new mixed algorithm, the mesoscaled behavior of the working fluid and the operation mechanism of a whole CPL can be investigated in detail, which can provide guidance for the design of a CPL system.