PROBLEM TO BE SOLVED: To provide a heating control system for an agricultural greenhouse by which circulation fans are efficiently operated in a control system different from a heater so as to achieve the reduction in fuel consumption, energy saving, and decrease in emission of combustion gas, and to provide a heating control method.SOLUTION: The heating control system for an agricultural greenhouse performs heating within a temperature fluctuation range from a lower limit temperature to a required temperature for growing crops in the agricultural greenhouse having a large-volume space. The system includes: a heater; a temperature sensor for control which has no electrical interconnection with the system of the heater and detecting temperature in the greenhouse; a plurality of circulation fans installed in the agricultural greenhouse; and a controller electrically connected with the temperature sensor for control and the circulation fans. The controller performs: a first step for driving the circulation fans just after driving the heater, and operating the circulation fans so as to have a setup rising temperature based on information from the temperature sensor for control; and a second step for operating the circulation fans until the following predetermined preset time period passes after receiving the information representing reaching the setup rising temperature from the temperature sensor for control.