The theoretical rational design of organic semiconductors faces an obstacle in that the performance of organic semiconductors depends very much on their stacking and local morphology (for example, phase domains), which involves numerous molecules. Simulation becomes computationally expensive as intermolecular electronic couplings have to be calculated from density functional theory. Therefore, developing fast and accurate methods for intermolecular electronic coupling estimation is essential. In this work, by developing a series of new intermolecular 3D descriptors, we achieved fast and accurate prediction of electronic couplings in both crystalline and amorphous thin films. Three groups of developed descriptors could perform faster and higher accuracy prediction on electronic couplings than the most advanced state-of-the-art descriptors. This work paves the way for large-scale simulations, high-throughput calculations, and screening of organic semiconductors.