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Background As thyroid fine needle aspiration (FNA) shows a certain limitation in the diagnosis of conventional smears, novel approaches like liquid-based cytology (LBC) have been gradually applied recently. Studies have shown the difference between the conventional smears (CSs) and liquid-based smears on fine needle aspiration cytology (FNAC) diagnosis, but the impacts of different liquid-based preparation (LBP) methods, including membrane-based and sedimentation, on diagnosis are still not clear. In this study, the effects of liquid-based smears prepared by different methods on the cytological interpretation were studied. Methods A total of 221 thyroid liquid-based FNAC cases from January 2017 to October 2018 were collected. We retrospectively studied and compared the effects of the membrane-based and sedimentation LBP methods through The Bethesda System for Reporting Thyroid Cytopathology (TBS) diagnosis and risk of malignancy assessment. Besides, we made an evaluation on the diagnostic differences in the effects of different preparation methods on the cell morphology and tissue structure of papillary thyroid carcinoma (PTC) for more accurate FNAC diagnosis. Results Among the 221 cases reviewed, membrane-based method was applied in 153 cases and sedimentation in 68 cases. According to the diagnostic criteria of 2017 TBS, TBSVI and TBSV thyroid could be cytologically diagnosed by membrane-based (49.0% (75/153) and 25.5% (39/153)) and sedimentation (52.9(36/68) and 25(17/68)) methods, and both were confirmed as PTC through histopathological diagnosis after operation, with the malignancy degree as high as 100%. In addition, of the 30 cases that were diagnosed as TBSIII thyroid nodules with the membrane-based method, 15 cases were pathologically malignant after an operation, with the malignancy degree of 50% (15/30), while that in 11 cases using the sedimentation method was 45.4% (5/11). PTC could be detected in both the TBSIV and TBSII thyroid nodules diagnosed by membrane-based method, with the sensitivity of 87.0% (114/131) lower than that by sedimentation method (91.4% (53/58)), showing the lower consistency with the histopathological result (K = 0.635 vs K = 0.757). Among the membrane-based smears, 23.5% (36/153) had fewer follicular epithelial cells, 55.6% (20/36) of which were considered to be suspicious for PTC from cell karyotype and tissue arrangement. While among the sedimentation smears, 16.2% (11/68) had fewer follicular epithelial cells, and 63.6% (7/11) was suspicious for PTC. In 72.5% (95/131) membrane-based smears of PTC, the papillary and swirling structures were not obvious, showing as crowded syncytial cell masses, while in 55.2% (32/58) sedimentation smears, both structures were visible with obvious three-dimensional papillary structure, and the fibrovascular axis still remained. Conclusion LBP technique is feasible for FNAC diagnosis, and the sedimentation shows more advantages, like higher PTC detection rate and good consistency with postoperative histopathological diagnosis. A clear understanding of the subtle differences in the effects of membrane-based and sedimentation methods on the cell morphology and tissue structure could be conducive to the definitive diagnosis of PTC before operation.