Marine atmospheric boundary-layer height (MABLH) is crucial for ocean heat, momentum, and substance transfer, affecting ocean circulation, climate, and ecosystems. Due to the unique geographical location of the South China Sea (SCS), coupled with its complex atmospheric environment and sparse ground-based observation stations, accurately determining the MABLH remains challenging. Coherent Doppler wind lidar (CDWL), as a laser-based active remote sensing technology, provides high-resolution wind profiling by transmitting pulsed laser beams and analyzing backscattered signals from atmospheric aerosols. In this study, we developed a stacking optimal ensemble model (SOEM) to estimate MABLH in the vicinity of the site by integrating CDWL measurements from a representative SCS site with ERA5 (fifth-generation reanalysis dataset from the European Centre for Medium-Range Weather Forecasts) data from December 2019 to May 2021. Based on the categorization of the total cloud cover data into weather conditions such as clear/slightly cloudy, cloudy/transitional, and overcast/rainy, the SOEM demonstrates enhanced performance with an average mean absolute percentage error of 3.7%, significantly lower than the planetary boundary-layer-height products of ERA5. The SOEM outperformed random forest, extreme gradient boosting, and histogram-based gradient boosting models, achieving a robustness coefficient (R2) of 0.95 and the lowest mean absolute error of 32 m under the clear/slightly cloudy condition. The validation conducted in the coastal city of Qingdao further confirmed the superiority of the SOEM in resolving meteorological heterogeneity. The predictions of the SOEM aligned well with CDWL observations during Typhoon Sinlaku (2020), capturing dynamic disturbances in MABLH. Overall, the SOEM provides a precise approach for estimating convective boundary-layer height, supporting marine meteorology, onshore wind power, and coastal protection applications.