The invention discloses a friction stir welding structure applied to a robot and a working method thereof, and relates to the technical field of friction stir welding equipment. The friction stir welding structure a shaft shoulder sleeve, a shaft shoulder, a main shaft connecting plate, a moving shaft connecting block, a stirring needle, an extension rod and a shaft shoulder locking nut, wherein the upper surface of the shaft shoulder sleeve is provided with the main shaft connecting plate, the shaft shoulder sleeve is connected with a robot friction stir welding main shaft through the main shaft connecting plate, the extension rod is arranged inside the shaft shoulder sleeve, a mounting hole is formed in the middle of the lower surface of the extension rod, the stirring needle is arrangedin the mounting hole, the lower end of the stirring needle protrudes downwards out of the shaft shoulder sleeve, a welding end is arranged at the lower end of the stirring needle, the shaft shoulderis arranged inside the lower end of the shaft shoulder sleeve, the lower end of the stirring needle penetrates through the shaft shoulder, a shaft shoulder pre-tightening hole position is formed in the lower end of the shaft shoulder sleeve, the shaft shoulder pre-tightening hole position is opposite to the shaft shoulder, and the locking nut is arranged in the shaft shoulder pre-tightening hole position. The friction stir welding structure has the characteristics of reducing the robot control difficulty, reducing the cost and improving the efficiency.