Botanical garden greenhouses typically use solar radiation as an important heat source and meanwhile provide light for plants to survive. However, in the summertime, when the solar radiation is too strong, overheating will occur in the greenhouse and natural ventilation assisted with shading is used to cool it down. The modulation strategy of shading is very important not only to indoor temperature but also to the growth of plants. In order to determine the control strategy of the shading area in the design and installation stage, a CFD model of an exhibition greenhouse in Shanghai is established. During summer conditions, under the worst-case scenario of a windless day, the minimum shading area needed under different outdoor comprehensive temperatures is studied, and the correlation curve is fitted to guide the control of the shading to maintain appropriate thermal conditions. The decrease in indoor temperature under different shading areas is also explored when the outdoor comprehensive temperature is 34 °C. The annual carbon emission reduction of the greenhouse is about 500 t CO2, by adopting shading and natural ventilation. This study provides a reference value for shading control and energy saving and emission reduction of a botanical garden greenhouse.