The invention discloses an indoor physical environment comprehensive control system. The system comprises a mobile control device, a controller, a gateway, an environment sensor, a terminal device anda cloud server, wherein the controller is connected with the cloud server through the gateway, is in wireless connection with the environment sensor, and is in wired or wireless connection with the terminal device, and the mobile control device is connected with the cloud server. According to the heat adaptation theory and the heat feeling of a user, the system performs comprehensive adjusting onthe indoor heat and humidity environment through adjusting the running state of the terminal device, and according to the theoretical comfortable range of illuminance, noise, PM2.5, PM10, CO2 and humidity, the indoor sound environment, the indoor light environment, the indoor wind environment and the indoor healthy environment are adjusted in the light of the sequence of health, comfort and energy conservation through adjusting the running state of the terminal device, so that the use experience of the user is improved, and meanwhile the considerable energy conservation effect is achieved.