This paper experimented with a methodology of machine learning modelling using virtual samples generated by a fast CFD (Computational Fluid Duy) simulations, in order to predict the greenhouse natural ventilation. However, the output natural ventilation rates using fast two-dimensional (2D) CFD models are not always consistent with the three-dimensional (3D) one for all the scenarios. The first contribution of this paper is a proposed comparative modelling methodology between two-dimensional and three-dimensional CFD (Computational Fluid Dynamics) studies, regarding its validity, especially when buildings are in rows. The results show that the error on the ventilation rate prediction could exceed 50%, if 2D models are not properly used. Subsequently, in those scenarios where the 2D and the 3D model had equal accuracy, nearly one thousand samples were generated using fast 2D CFD simulations to train natural ventilation rate regression tree-model. This model is efficient to deal with the combined effect of wind pressure and thermal gradients under various vent configurations, with only four necessary inputs. In addition, by analyzing the wind speed distribution contour of the outdoor wind field around the greenhouse rows, the optimal wind speed measuring locations were determined to eliminate interference for predicting the natural ventilation rate.