The invention relates to a mobile acquisition control system and a control method of the mobile acquisition control system. The main technical feature is that the system comprises at least one piece of data acquisition equipment, a serial server and mobile equipment having a wireless communication function, wherein the data acquisition equipment is in communication connection with the serial server through a serial bus, the serial server is in communication connection with the mobile equipment, the method comprises acquiring the IP addresses of the serial server and each data acquisition equipment by the mobile equipment, sending a downlink message by the mobile equipment to the target data acquisition equipment through the communication network and the serial server, receiving the return code transmitted back from the data acquisition equipment, and executing corresponding operation by the target data acquisition equipment according to the content of the downlink message after receiving the downlink message transmitted by the mobile equipment. According to the mobile acquisition control system, the serial server serves as a media to correlate the data acquisition equipment and the mobile equipment, the data acquisition is conducted through the control over the mobile equipment, so that the user affinity of the product is greatly improved.