Multiple Instance Learning (MIL) in digital pathology Whole Slide Image (WSI) analysis has shown significant progress. However, due to data bias and unobservable confounders, this paradigm still faces challenges in terms of performance and interpretability. Existing MIL methods might identify patches that do not have true diagnostic significance, leading to false correlations, and experience difficulties in integrating multi-scale features and handling unobservable confounders. To address these issues, we propose a new Multi-Scale Frequency Domain Causal framework (MFC). This framework employs an adaptive memory module to estimate the overall data distribution through multi-scale frequency-domain information during training and simulates causal interventions based on this distribution to mitigate confounders in pathological diagnosis tasks. The framework integrates the Multi-scale Spatial Representation Module (MSRM), Frequency Domain Structure Representation Module (FSRM), and Causal Memory Intervention Module (CMIM) to enhance the model's performance and interpretability. Furthermore, the plug-and-play nature of this framework allows it to be broadly applied across various models. Experimental results on Camelyon16 and TCGA-NSCLC dataset show that, compared to previous work, our method has significantly improved accuracy and generalization ability, providing a new theoretical perspective for medical image analysis and potentially advancing the field further. The code will be released at https://github.com/WissingChen/MFC-MIL.