Accurate assessments are vital for the effective conservation of desert steppe ecosystems, which are essential for maintaining biodiversity and ecological balance. Although geostatistical methods are commonly used for spatial modeling, they have limitations in terms of feature extraction and capturing non-linear relationships. This study therefore proposes a novel remote sensing framework that integrates geostatistical methods and machine learning to predict the Shannon-Wiener index in desert steppe. Five models, Kriging interpolation, Random Forest, Support Vector Machine, 3D Convolutional Neural Network and Graph Attention Network, were employed for parameter inversion. The Helmert variance component estimation method was introduced to integrate the model outputs by iteratively evaluating residuals and assigning relative weights, enabling both optimal prediction and model contribution quantification. The ensemble model yielded a high prediction accuracy with an R2 of 0.7609. This integration strategy improves the accuracy of index prediction, and enhances the interpretability of the model regarding weight contributions in space. The proposed framework provides a reliable, scalable solution for biodiversity monitoring and supports scientific decision-making for grassland conservation and ecological restoration.