The timing control system is an indispensable part of cold atom interference experiment, gravimeter development and application test. It is responsible for coordinating, driving and controlling the operation of each subsystem, and is the central unit of cold atom interference control. Aiming at the timing control requirements of high-precision regulation, multi-channel synchronization and flexible regulation in the process of cold atom interference, a set of programmable timing control system for cold atom interference is designed and implemented based on ARM+FPGA architecture, which is composed of timing master module and multiple slave device modules, and has the functions of synchronous trigger, analog modulation, RF drive, signal acquisition and data processing. The results of system test and cold atom interference experiment show that the timing adjustment accuracy of the system can reach 10 ns, and the control accuracy and multi-channel synchronization accuracy are better than 2 ns, which meets the application requirements of cold atom interference timing control and is successfully used in cold atom interference gravity measurement.