Carbon fiber reinforced polymer (CFRP) is widely used in aircraft panel structures. Due to molding process constraints, there are varying degrees of assembly gaps at component interfaces. In engineering practice, when the gap exceeds a certain threshold, gap-compensation measures are required. The panel assembly experiences complex deformation and stress concentration after gap compensation, affecting subsequent aircraft operational performance. Therefore, simulation analysis and experimental verification on the impact of bolt fastening sequences on CFRP panel assembly quality after gap filling are conducted. Analysis reveals that the panel offsets with a rotational deformation centered at the upper right endpoint towards the lower left. Normal deformations occur on both sides of the panel and around the bolt holes, with the maximum normal deformation value decreasing by approximately 63.4% when changing the bolt fastening sequence. The fastening sequence has a minor influence on the overall stress distribution of the panel, while significantly affects the stress distribution around the bolt holes and the distribution of panel assembly deformations, favoring symmetric joining over sequential joining. The stress distribution around the holes is closely related to the gap span and amount, increasing in magnitude and range as the gap amount rises.