The food security of more than half of the world’s population depends on rice production which is one of the key objectives of precision agriculture. The traditional rice almanac used astronomical and climate factors to estimate yield response. However, this research integrated meteorological, agro-chemical, and soil physiographic factors for yield response prediction. Besides, the impact of those factors on the production of three major rice ecotypes has also been studied in this research. Moreover, this study found a different set of those factors with respect to the yield response of different rice ecotypes. Machine learning algorithms named Extreme Gradient Boosting (XGBoost) and Support Vector Regression (SVR) have been used for predicting the yield response. The SVR shows better results than XGBoost for predicting the yield of the Aus rice ecotype, whereas XGBoost performs better for forecasting the yield of the Aman and Boro rice ecotypes. The result shows that the root mean squared error (RMSE) of three different ecotypes are in between 9.38% and 24.37% and that of R-squared values are between 89.74% and 99.13% on two different machine learning algorithms. Moreover, the explainability of the models is also shown in this study with the help of the explainable artificial intelligence (XAI) model called Local Interpretable Model-Agnostic Explanations (LIME).