Absorption imaging is the foundation for quantitative measurements in experiments on ultracold atoms. This technique mainly involves capturing images of both the probing light field and the atom absorption light field. In this process, the unavoidable jitter of the probing light introduces imaging noise of fringe patterns into the atomic optical density distribution OD. In conventional fringe removal algorithms, this type of noise can be normalized by constructing an optimal reference image from multiple reference images that have been actually taken, which shares similar fringe patterns to an absorption image (Fig. (a)). Although this method works well in the region without atomic signal, they often overlook the modulation of the noise signal due to atomic absorption effects, leading to persistent residual fringes on the atom clouds. This problem becomes more pronounced with atomic density increasing. Here, we propose an enhanced fringe removal algorithm that takes into account the effects of atomic absorption, and actively modulates the intensity of the noise signal in the reference image constructed by conventional fringe removal algorithms (Fig. (b)), effectively preventing the residual fringes from forming, thus significantly improving the signal-to-noise ratio of the atomic images. When applied to the absorption imaging of homogeneous Fermi gases with high density, as shown in Fig. (d), this new algorithm successfully reduces the relative standard deviation of optical depth characterizing atomic density fluctuations by approximately 37%, which is about 3 times the relative standard deviation by conventional algorithm. Three subgraphs in Fig. (e) show the optical depth distribution at corresponding data points labeled by square boxes in Fig. (d). Furthermore, we also use this technique to quantitatively determine the second sound in the unitary Fermi superfluid of ⁶Li atoms. Compared with conventional fringe removal methods, our new algorithm increases the correlation function’s contrast of the density wave nearly 4 times, therefore enhancing the intensity of the density response spectrum by approximately 15% with half the measured standard error, paving the way for quantitatively determining the speed and attenuation of the second sound. These results demonstrate that the enhanced fringe removal algorithm not only effectively suppresses fringe noise, but also facilitates the identification and detection of important physical phenomena in high-density atomic systems, such as some collective excitations and new quantum phases.