Aluminum alloy thin-walled disk components, as the core structure of a satellite detector antenna, require extremely high flatness, and the current milling level often fails to meet design requirements. To address the issue of excessive deformation of 7A04 aluminum alloy thin-walled disk during milling caused by residual stress coupling effects, a deformation suppression method integrating structural design and process control was proposed. First, the distribution patterns of initial internal stresses and milling residual stress gradients in 7A04 aluminum alloy were obtained. Second, using the Abaqus finite element platform, a deformation simulation model for the thin-walled disk under the coupled effects of initial/milling residual stresses was established. Then, a deformation-resistant optimization design for the 7A04 aluminum alloy thin-walled disk structure was conducted. Finally, through thin-walled disk machining experiments, the effectiveness of the structural optimization scheme was verified, and it was found that the flatness of the thin-walled disk reached 0.103 mm. Consequently, a collaborative control methodology comprising “stress distribution detection-deformation simulation modelling-deformation-resistant structural design” was formed. This approach effectively suppresses coupled deformation arising from initial and residual milling stresses, providing an effective technical solution for the precision manufacturing of aerospace thin-walled components.