The combined use of multiple modalities enables accurate pedestrian detection under poor lighting conditions by using the high visibility areas from these modalities together. The vital assumption for the combination use is that there is no or only a weak misalignment between the two modalities. In general, however, this assumption often breaks in actual situations. Due to this assumption's breakdown, the position of the bounding boxes does not match between the two modalities, resulting in a significant decrease in detection accuracy, especially in regions where the amount of misalignment is large. In this paper, we propose a multi-modal Faster-RCNN that is robust against large misalignment. The keys are 1) modal-wise regression and 2) multi-modal IoU for mini-batch sampling. To deal with large misalignment, we perform bounding box regression for both the RPN and detection-head with both modalities. We also propose a new sampling strategy called "multi-modal mini-batch sampling" that integrates the IoU for both modalities. We demonstrate that the proposed method's performance is much better than that of the state-of-the-art methods for data with large misalignment through actual image experiments.