Pump–probe thermoreflectance has been commonly applied for characterizing the thermal properties of materials. Generally, a reliable and efficient non-linear fitting process is often implemented to extract unknown thermal parameters during the pump–probe thermoreflectance characterizations. However, when it comes to processing large amounts of data acquired from similar structural samples, non-linear fitting process appears to be very time-consuming and labor-intensive to search for the best fitting for every testing curve. Herein, we propose to apply deep learning (DL) approach to nanosecond transient thermoreflectance technique for high-throughput experimental data processing. We first investigated the effect of training set parameters (density and bounds) on the predictive performance of the DL model, providing a guidance to optimize the DL model. Then, the DL model is further verified in the measurement of the bulk sapphire, SiC, diamond samples, and GaN-based multilayer structures, demonstrating its capability of analyzing the results with high accuracy. Compared to the conventional non-linear fitting method (such as Global Optimization), the computation time of the new model is 1000 times lower. Such a data-driven DL model enables the faster inference and stronger fitting capabilities and is particularly efficient and effective in processing data acquired from wafer-level measurements with similar material structures.