The invention discloses a vehicle-mounted drone control system and a control method thereof. The vehicle-mounted drone control system comprises a square pipe launching bin, an extension section, an electric rotary platform, a PLC and a terminal, the head end of the square pipe launching bin is hinged to the electric rotary platform, a drone position probing device is arranged in the square pipe launching bin, an obstacle senor is arranged at the tail end of the square pipe launching bin, a first electric guide rail is embedded onto the inner bottom face of the square pipe launching bin, a second electric guide rail is embedded onto the outer bottom face of the square pipe launching bin, a following plate is arranged on the first electric guide rail, guiding openings matched with drone wings are formed in both the left side wall and the right side wall of the square pipe launching bin, ball rows are arranged in the guiding openings, a dovetail groove is formed in the outer bottom face of the square pipe launching bin, and a dovetail joint matched with the dovetail groove is arranged on the extension section, and is inserted into the dovetail groove. The vehicle-mounted drone controlsystem is high in automated degree.