Adjoint optimization method is used to optimize the drag reduction design of long-endurance UAV fuselage, and FFD free surface deformation technology is used for grid deformation. According to the self-definition global variable function of fuselage shape, the displacement of each control point in yz two directions is realized by single degree adjoint calculation, and the deformation of fuselage surface is completed under the transitional smooth condition. In order to ensure the symmetry of the fuselage, only the left half module is deformed after the adjoint solution, and the control points of the right half module are constrained by mirroring variables. At the upper and lower limits of global variables, the deformation amplitude of definition control point is 10% of the distance from fuselage axis to surface, so there is no need to set additional thickness constraints on adjoint optimization. After smoothing the shape of the accompanying program output, the drag reduction of the final configuration fuselage parts is 6.77%, which is equivalent to 2.04% of the whole aircraft drag reduction effect. Q criterion is used to characterize the coherent structure with small scale in the flow field. adjoint optimization weakens the vortex structure around the fuselage, which characterizes the rotation effect of the flow field, and makes the flow more stable. The normal Mach number Man isosurface is used to characterize the region with large pressure gradient and shock wave tendency in the flow field. adjoint optimization significantly reduces the region with large pressure gradient between fuselage and tail, and weakens the pressure fluctuation between fuselage and tail.