The invention discloses a flow sub-weighing system with a dustproof cover plate and an automatic baffle, which comprises a weighing chamber and a first cylinder groove. A dye warehouse is arranged below the weighing chamber; a chute platform is arranged below the dye warehouse; a dye platform is arranged inside the dye warehouse; an induction lamp and an automatic baffle are mounted on the front surface of the dye warehouse at an equal distance; a trolley is arranged right in front of the dye warehouse; a bedplate is arranged on the trolley; the bedplate is connected with the dustproof cover plate through a second cylinder; a fixed block is arranged on both sides of the bottom of the trolley; one end of the fixed block is connected with the first cylinder; the first cylinder is mounted inthe first cylinder groove; and a connection rod is arranged at both ends of the back of the trolley. The flow sub-weighing system with a dustproof cover plate and an automatic baffle not only has reasonable design, simple structure and convenience for operations but also greatly reduces the possibility of dye pollution, thereby facilitating temperature control and humidity control, ensuring the safety of the staff, and improving the working efficiency.