With the development of broadband networks and high-definition displays, people have higher expectations for the quality of video images, which also brings new requirements and challenges to video coding technology. Compared with H.265/High Efficiency Video Coding (HEVC), the latest video coding standard, Versatile Video Coding (VVC), can save 50%-bit rate while maintaining the same subjective quality, but it leads to extremely high encoding complexity. To decrease the complexity, a fast coding unit (CU) size decision method based on Just Noticeable Distortion (JND) and deep learning is proposed in this paper. Specifically, the hybrid JND threshold model is first designed to distinguish smooth, normal, or complex region. Then, if CU belongs to complex area, the Ultra-Spherical SVM (US-SVM) classifiers are trained for forecasting the best splitting mode. Experimental results illustrate that the proposed method can save about 52.35% coding runtime, which can realize a trade-off between the reduction of computational burden and coding efficiency compared with the latest methods.