The stratified soil temperature control and heat storage system is carried out for greenhouses in Northeast China, increasing the temperature of plant root zone and storing heat in the soil. The effects of root water absorption and irrigation are considered to analyze the variation characteristics of the soil temperature quantitatively in complex dynamic heat transfer mechanisms, and the root zone temperature is also used as an evaluation criterion to explore the effect of soil temperature on plant growth during the continuous system operation. The results illustrate that the soil temperature is measured to increase significantly. The soil temperatures of the temperature-controlled zone are maintained in the optimal range for plant growth throughout the T2 phase from 15 to 30 days. And the temperature distribution is developed to be spatially uniform as the temperature difference of each position is less than 2%. These results are demonstrated to be effective in fulfilling the developmental requirements of cultivated plants.