Objective: Precise classification of mass-forming intrahepatic cholangiocarcinoma (MF-ICC) and hepatocellular carcinoma (HCC) based on magnetic resonance imaging (MRI) is crucial for personalized treatment strategy. The purpose of the present study was to differentiate MF-ICC from HCC applying a novel deep-learning-based workflow with stronger feature extraction ability and fusion capability to improve the classification performance of deep learning on small datasets. Methods: To retain more effective lesion features, we propose a preprocessing method called semi-segmented preprocessing (Semi-SP) to select the region of interest (ROI). Then, the ROIs were sent to the strided feature fusion residual network (SFFNet) for training and classification. The SFFNet model is composed of three parts: the multilayer feature fusion module (MFF) was proposed to extract discriminative features of MF-ICC/HCC and integrate features of different levels; a new stationary residual block (SRB) was proposed to solve the problem of information loss and network instability during training; the attention mechanism convolutional block attention module (CBAM) was adopted in the middle layer of the network to extract the correlation of multi-spatial feature information, so as to filter the irrelevant feature information in pixels. Results: The SFFNet model achieved an overall accuracy of 92.26% and an AUC of 0.9680, with high sensitivity (86.21%) and specificity (94.70%) for MF-ICC. Conclusion: In this paper, we proposed a specifically designed Semi-SP method and SFFNet model to differentiate MF-ICC from HCC. This workflow achieves good MF-ICC/HCC classification performance due to stronger feature extraction and fusion capabilities, which provide complementary information for personalized treatment strategy.