Generally, windows in greenhouses are automatically opened and closed to regulate the internal temperature. However, because the air outside during the winter in Japan is dry, opening windows to reduce the temperature causes the humidity deficit to increase above 6 g/m3, thereby inhibiting plant growth. Therefore, in this study, we developed a model that considers the effects of weather and the sampling period using a subspace (N4SID) method based on environmental data from inside and outside a greenhouse during winter. By adopting a data-driven model, models for greenhouse temperature and humidity deficits can be constructed conveniently. First, four models incorporating weather conditions were constructed over a 28-day modelling period. Moreover, the average root mean square error values from 8:00 to 16:00 during the 10-day model evaluation period were examined. Subsequently, model predictive controllers were developed from the four models with sampling periods of 1, 2, 4, and 8 min, and their performances were compared over the model evaluation period. The model predictive controller with a sampling period of 4 min was the most energy-efficient, achieving control of the humidity deficit of up to at most 6 g/m3 (close to the target value of 4.5 g/m3) while maintaining the target temperature of 26 °C.