The invention relates to a multi-thread data acquisition system synchronization control method in an acquisition time control mode, and belongs to the ground penetrating radar detection technology field. The method comprises the following steps: three time control variables (hour, minute, second) are established as a preset acquisition time and are inputted into a timer; a timing result with other two control variables serve as an information interaction carrier among independent threads and carry out a Boolean operation, and a result of the Boolean operation serves as a synchronization control signal of different threads; the multi-thread synchronization control in the mode is realized through a control variable assignment and a corresponding criterion function; and furthermore, a preset criterion function of the threads is written in so as to realize storage of all acquisition data. The method of the invention is based on the computer control theory, and the control function of the ground penetrating radar multi-thread acquisition system is realized.