The invention discloses an automatic operating base station for a plant protection unmanned aerial vehicle. The automatic operating base station comprises a base station (1), a dosing pump (2), a storage tank (3), a control module (4), a dosing module (5) arranged in the base station (1), a positioning push rod module (6) arranged at the top of the base station (1), a battery picking and placing module (7) arranged on the right side of the base station (1), a vertical motion module (8), a horizontal motion module (9), an intelligent rechargeable battery compartment module (10) and a support (11), wherein the dosing module (5) comprises an outer pipe (15), a dosing cylinder (16), a rising positioning cylinder (17), a vertical buffer limit spring (18), a spring fixing seat (19), a straight pipe (20), a dosing head (21) and a conical head (22) located in a through hole; and the automatic operating base station further comprises a gas source module (37) and a power module (38). The automatic operating base station has the advantages that the working efficiency of the plant protection unmanned aerial vehicle is improved, the plant protection unmanned aerial vehicle is automatically dosed and charged, and the degree of automation is high.