A vacuum excrement collector control system and device thereof are disclosed. The control system comprises a program controller, the program controller is connected with a master control system, the connecting end of the master control system is connected with a regulating valve, a pressurization system, a vacuum generator and a blow-down valve, and the output end of the pressurization system is connected with a water-vapor mixed flowing-out device. The vacuum generator is connected with a storage tank, the storage tank is respectively provided with a sewage suction port and a sewage discharge port, the sewage discharge port is connected with a sewage discharge pipe, and when the vacuum excrement collector system operates, the touch program controller enables the master control system to respectively regulate and control the regulating valve, the pressurization system and the vacuum generator, the pressurization system enables the water-emulsion liquid to be sprayed out at a high speed through the water-vapor mixing and flowing-out device, oxygen is released, and dirt is discharged into the storage tank through the dirt suction opening. Compared with a traditional pump station type vacuum system, the control system and the device thereof are low in manufacturing cost, space is saved, and normal work of other toilet cubicles is not influenced when a single toilet cubicle is damaged.