A rotary screen transfer printing machine and a control system thereof. The rotary screen transfer printing machine having a feeding unit, a printing unit, a drying unit, and a receiving unit; the printing unit has at least one rotary screen transfer printing assembly and a guide belt assembly; each rotary screen transfer printing assembly has a rotary screen plate roller and a transfer roller; the rotary screen plate roller is close to the transfer roller; the transfer roller is seamlessly coated with rubber or a resin having good affinity for a water-based ink. A control system includes: a motion controller; a conveying synchronization module, used for controlling the feeding unit, the printing unit, the drying unit, and the receiving unit to synchronize the conveying speeds of the four units; and a rotary screen transfer printing synchronization module.