The effective estimation of mixed-layer depth (MLD) plays a significant role in the study of ocean dynamics and global climate change. However, the methods of estimating MLD still have limitations due to the sparse resolution of the observed data. In this study, a hybrid estimation method that combines the K-means clustering algorithm and an artificial neural network (ANN) model was developed using sea-surface parameter data in the Indian Ocean as a case study. The oceanic datasets from January 2012 to December 2019 were obtained via satellite observations, Argo in situ data, and reanalysis data. These datasets were unified to the same spatial and temporal resolution (1° × 1°, monthly). Based on the processed datasets, the K-means classifier was applied to divide the Indian Ocean into four regions with different characteristics. For ANN training and testing in each region, the gridded data of 84 months were used for training, and 12-month data were used for testing. The ANN results show that the optimized NN architecture comprises five input variables, one output variable, and four hidden layers, each of which has 40 neurons. Compared with the multiple linear regression model (MLR) with a root-mean-square error (RMSE) of 5.2248 m and the HYbrid-Coordinate Ocean Model (HYCOM) with an RMSE of 4.8422 m, the RMSE of the model proposed in this study was reduced by 27% and 22%, respectively. Three typical regions with high variability in their MLDs were selected to further evaluate the performance of the ANN model. Our results showed that the model could reveal the seasonal variation trend in each of the selected regions, but the estimation accuracy showed room for improvement. Furthermore, a correlation analysis between the MLD and input variables showed that the surface temperature and salinity were the main influencing factors of the model. The results of this study suggest that the pre-clustering ANN method proposed could be used to estimate and analyze the MLD in the Indian Ocean. Moreover, this method can be further expanded to estimate other internal parameters for typical ocean regions and to provide effective technical support for ocean researchers when studying the variability of these parameters.