Most of the industrial processes are multivariable in nature. Greenhouse system is considered which the important application is in agricultural process. Greenhouse is to improve the environmental conditions in which plants are grown. In this paper, the authors have proposed identification of greenhouse system using input and output data sets to estimate the best model and validate the model. For MIMO systems, Neural Network System identification provides a better alternative to find their system transfer function. The results were analyzed and the model is obtained. From this obtained model, the system is controlled by conventional method. By in this method they can identify the model and control the complicated systems like Greenhouse.