The invention discloses a double-pump multi-path high-precision filling device and a control method thereof. The double-pump multi-path high-precision filling device comprises a controller, a double-pump mechanism and a multi-path filling mechanism, wherein the double-pump mechanism and the multi-path filling mechanism are connected between a medicament jar and a multi-path main flow pipeline in sequentially; the double-pump mechanism comprises a conventional filling pump branch and a standby filling pump branch which are connected in parallel; the fluid outlet of the double-pump mechanism isconnected with the medicament jar by virtue of a backflow mechanism; the controller is a PLC (Programmable Logic Controller); the PLC comprises a double-pump control module and a solenoid valve on-off control module; the solenoid valve on-off control module is used for controlling the on and off of a solenoid valve; and the double-pump control module is used for controlling the conventional filling pump and the standby filling pump to act. Thus, a reliable double-pump control method is adopted by the double-pump multi-path high-precision filling device, two gear pumps are shared, the load is balanced, and the two gear pumps are in mutual standby application, thereby achieving high reliability. In the double-pump multi-path high-precision filling device, the solenoid valve on-off control based on a PID-PWM (Proportion Integration Differentiation- Pulse-Width Modulation) filling pulse control method is adopted, the filling precision is high, the synchronization performance with main flow is good, and the phenomena of repeated adding and missed adding can be effectively avoided.