As energy heating is one of the main production costs, many efforts have been made to reduce the energy consumption of agricultural greenhouses. Herein, a novel control method of greenhouse heating using computational fluid dynamics (CFD) and energy prediction model (EPM) is proposed for energy savings and system performance. Based on the low-Reynolds number k-epsilon turbulence principle, a CFD model of heating greenhouse is developed, applying the discrete ordinates model for the radiative heat transfers and porous medium approach for plants considering plants sensible and latent heat exchanges. The CFD simulations have been validated, and used to analyze the greenhouse thermal performance and the priority of fan coil units (FCU) loops under the various heating conditions. According to the heating efficiency and temperature uniformity, the priorities of each FCU loop can be predicted to generate a database with priorities for control system. EPM is built up based on the thermal balance, and used to predict and optimize the energy demand of the greenhouse online. Combined with the priorities of FCU loops from CFD simulations offline, we have developed the CFD-EPM-based heating control system of greenhouse with surface water source heat pumps system (SWSHPS). Compared with conventional multi-zone independent control (CMIC) method, the energy savings potential is between 8.7% and 15.1%, and the control temperature deviation is decreased to between 0.1 degrees C and 0.6 degrees C in the investigated greenhouse. These results show the CFD-EPM-based method can improve system performance with more accurate temperature, more rapid responses and lower energy consumption. (C) 2014 Elsevier Ltd. All rights reserved.