The Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) is equipped with the Advanced Topographic Laser Altimeter System (ATLAS), which can achieve high-precision ground detection. However, due to its low pulse energy and high sensitivity, it is also affected by noise when obtaining data. Therefore, data denoising is critical to the subsequent processing and application. In this study, a multilevel filtering algorithm is proposed to denoise the daytime photon cloud data with high background noise. Firstly, the Random Sample Consensus (RANSAC) algorithm is used to roughly denoise the daytime photon cloud data with high background noise, and a signal point cloud buffer is established to remove most of the noise points. Subsequently, the horizontal continuity parameter is calculated based on the photon cloud data following the rough denoising process. Based on this parameter, the shape and size of the search domain of the results of the subsequent fine denoising algorithm are adaptively improved. Finally, three filtering directions (a horizontal direction, an intra-group unified direction, and an adaptive direction for each photon) are proposed, and a hybrid algorithm combining the Ordering Points to Identify the Clustering Structure (OPTICS) density clustering algorithm and the Relative Neighboring Relationship K-nearest neighbors-based noise removal (RNR−KNNB) algorithm is employed to accurately denoise the photon cloud data in the three filtering directions. Furthermore, the RANSAC algorithm based on a sliding overlap window is used to remove outliers for the weak beam fine denoising photon cloud data. The results indicate that, for the strong beams, the denoising accuracy of the multilevel filtering algorithm in the three filtering directions is comparable (Rs ≥ 0.96, F ≥ 0.67), and they are all better than that of the ATL08 algorithm (Rs/Rn/p/F = 0.85/0.67/0.52/0.65). For weak beams, the denoising accuracy of the multilevel filtering algorithm in the horizontal direction and the intra-group unified direction is similar (Rs = 0.92, F = 0.69), and it is superior to the denoising results in the adaptive direction of each photon and the ATL08 algorithm (Rs/Rn/p/F = 0.94/0.84/0.51/0.65, 0.88/0.87/0.55/0.67, respectively). For strong and weak beams, the p-value and F-value of the denoising results of multilevel filtering algorithms in three different filtering directions increase with the increase of SNR value. It is demonstrated that SNR is an important factor affecting the denoising results of algorithms. The multilevel filtering algorithm proposed in the study can effectively achieve precise denoising of daytime photon cloud data with high background noise, and the three different filtering directions have different effects on the denoising results of strong and weak beam photon cloud data. This can provide technical and methodological guidance for subsequent photon cloud data filtering processing.