It is very important that the comfortable indoor climate is built for crop growing in greenhouse. To adjust the temperature and humidity, the natural ventilation operation and indoor airflow operation is necessary to be controlled. Depending on many researches and analysis for indoor climate of greenhouse, it is proved that the two main parameters, temperature and humidity in greenhouse, correlate with ventilation, and the relation equation is indicated tunambiguous. On the other hand, there is other research which indicates that the growth result of crop is affected by the ways of airflow in greenhouse as well as natural ventilation. For all of these factors, with advance control theory and intelligent control technology, the control system of natural ventilation is presented in this paper. The main point in the paper is that depending on replacement ventilation principle the natural ventilation will be controlled by driving the windows open. First, the ventilation model using in greenhouse is constructed specially using actuators for driving windows one by one, and control model is analyzed on the principle of natural ventilation too. It is present firstly that using fuzzy control method depending on the temperature indoor to drive windows to work is feasible. Then the system designing of driving windows is given, and the intelligentized controlling system for natural ventilation in greenhouse is constructed finally. According to the smart fuzzy calculating and crop growth need condition, the windows open angle can be controlled accurately with detecting indoor parameters such as temperature, humidity, CO2 density as well as outdoor temperature, sun light, wind and rain. Also, the characteristic and designing factors used in this control system, with one example, are shown in this paper.