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Objectives: To retrospectively compare multilevel volumetric changes in both hard and soft tissues between antral pseudocyst (AP) removal and retainment before maxillary sinus floor augmentation (MSFA) and immediate implant placement. Material and methods: Twenty‐six patients with 38 implants placed from 2016 to 2021 were included and divided according to a cohort design as follows: 13 removing the cyst (RC group) and 13 "leaving alone" the cyst (LC group). 3D radiographic parameters (primary outcome), 2D parameters and clinical records (secondary outcome) involving both hard and soft tissues were evaluated for four periods (T1: immediate postoperative, T2: 6‐month, T3: 12‐month, and T4: 2‐ to 5‐ year follow‐up). Possible confounding factors, including sinus anatomical features and implant distribution, were also analyzed to eliminate their disturbance. Results: The 3D volumetric change rate of bone grafts in the RC group (−9.32% ± 10.01%) from T2 to T3 was significantly lower than that in the LC group (−19.8% ± 10.59%) (p <.05). The change rate of apical bone height (ABH), endo‐sinus bone gain (ESBG) and other 2D parameters were not significantly different between the two groups. 5.3% implants in RC group and 9.1% implants in LC group failed during follow‐ups. 0% postoperative complications were observed in RC group. The Schneiderian membrane of RC group was significantly thinner than that of LC group at two measuring points in sinus. Conclusion: The present study demonstrated that compared to AP retainment, AP removal before MSFA and immediate implant placement can obtain higher bone graft volumetric stability and favorable prognosis. [ABSTRACT FROM AUTHOR]