The aim is to reduce the elastic deformation of the web and side walls of low-stiffness thin-walled beams when the floating fixture method is used. This paper takes the number and position of fixture points as the optimization variables, establishes a calculation model of elastic deformation, and constructs the objective function of maximum total elastic deformation. An optimized solution utilizing the augmented multiplier method is employed, which forms the basis for the fixture layout optimization method to reduce the elastic deformation of low-stiffness thin-walled beams. A theoretical calculation, simulation analysis, and the fixture layout optimization of total maximum elastic deformation were completed using an aluminum alloy low-stiffness thin-walled beam as an example. The results show that based on the optimized layout, the average relative error between the calculated value and the simulated value of total maximum elastic deformation is 17.43%, and the simulated value of maximum elastic deformation is reduced by 48.49% after optimizing the fixture layout. The measured value is reduced by 0.02 mm on average, and deformation is reduced by 74.07%, which verifies the effectiveness of the floating fixture layout optimization control of machining elastic deformation proposed in this paper.