Global cloud thermodynamic phase (CP) is normally derived from polar-orbiting satellite imaging data with high spatial resolution. However, constraining conditions and empirical thresholds used in the MODIS (Moderate Resolution Imaging Spectroradiometer) CP algorithm are closely associated with spectral properties of the MODIS infrared (IR) spectral bands, with obvious deviations and incompatibility induced when the algorithm is applied to data from other similar space-based sensors. To reduce the algorithm dependence on spectral properties and empirical thresholds for CP retrieval, a machine learning (ML)-based methodology was developed for retrieving CP data from China’s new-generation polar-orbiting satellite, FY-3D/MERSI-II (Fengyun-3D/Moderate Resolution Spectral Imager-II). Five machine learning algorithms were used, namely, k-nearest-neighbor (KNN), support vector machine (SVM), random forest (RF), Stacking and gradient boosting decision tree (GBDT). The RF algorithm gave the best performance. One year of EOS (Earth Observation System) MODIS CP products (July 2018 to June 2019) were used as reference labels to train the relationship between MODIS CP (MYD06 IR) and six IR bands of MERSI-II. CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization), MODIS, and FY-3D/MERSI-II CP products were used together for cross-validation. Results indicate strong spatial consistency between ML-based MERSI-II and MODIS CP products. The hit rate (HR) of random forest (RF) CP product could reach 0.85 compared with MYD06 IR CP products. In addition, when compared with the operational FY-3D/MERSI CP product, the RF-based CP product had higher HRs. Using the CALIOP cloud product as an independent reference, the liquid-phase accuracy of the RF CP product was higher than that of operational FY-3D/MERSI-II and MYD06 IR CP products. This study aimed to establish a robust algorithm for deriving FY-3D/MERSI-II CP climate data record (CDR) for research and applications.