This research presents a comprehensive analysis of various imputation methods for addressing missing microclimate data in the context of coffee-pine agroforestry land in UB Forest. Utilizing Big data and Machine learning methods, the research evaluates the effectiveness of imputation missing microclimate data with Interpolation, Shifted Interpolation, K-Nearest Neighbors (KNN), and Linear Regression methods across multiple time frames - 6 hours, daily, weekly, and monthly. The performance of these methods is meticulously assessed using four key evaluation metrics Mean Absolute Error (MAE), Mean Squared Error (MSE), Root Mean Squared Error (RMSE), and Mean Absolute Percentage Error (MAPE). The results indicate that Linear Regression consistently outperforms other methods across all time frames, demonstrating the lowest error rates in terms of MAE, MSE, RMSE, and MAPE. This finding underscores the robustness and precision of Linear Regression in handling the variability inherent in microclimate data within agroforestry systems. The research highlights the critical role of accurate data imputation in agroforestry research and points towards the potential of machine learning techniques in advancing environmental data analysis. The insights gained from this research contribute significantly to the field of environmental science, offering a reliable methodological approach for enhancing the accuracy of microclimate models in agroforestry, thereby facilitating informed decision-making for sustainable ecosystem management.