The use of photon counting detectors in X-ray imaging missions can effectively improve the signal-to-noise ratio and image resolution. However, the stitching of photon counting detector modules leads to large-size localized information loss in the acquired projected image, which seriously affects the regional observation. In this paper, we propose a method to fill the inter-module gap based on dual acquisition, referred to as the GFDA algorithm, which is divided into three main steps: (i) acquire the main projection by short-exposure scanning, and then scan again by vertically moving the carrier table to acquire the reference projection; (ii) use the alignment method to locate the projected region of interest; (iii) use image stitching and image fusion to recover the missing information. We analyzed the gray value of the region of interest of the Siemens star projection and the reconstructed conch slice data, and proved that the proposed method can recover the information more smoothly and perfectly. The GFDA algorithm is able to achieve a better image restoration effect without additional scanning time and better retain image details. In addition, the GFDA algorithm is scalable, which is demonstrated in the task of filling the stitching of multiple types of photonic technology detectors.