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Integrating multispectral data in object detection, especially visible and infrared images, has received great attention in recent years. Since visible (RGB) and infrared (IR) images can provide complementary information to handle light variations, the paired images are used in many fields, such as multispectral pedestrian detection, RGB-IR crowd counting and RGB-IR salient object detection. Compared with natural RGB-IR images, we find detection in aerial RGB-IR images suffers from cross-modal weakly misalignment problems, which are manifested in the position, size and angle deviations of the same object. In this paper, we mainly address the challenge of cross-modal weakly misalignment in aerial RGB-IR images. Specifically, we firstly explain and analyze the cause of the weakly misalignment problem. Then, we propose a Translation-Scale-Rotation Alignment (TSRA) module to address the problem by calibrating the feature maps from these two modalities. The module predicts the deviation between two modality objects through an alignment process and utilizes Modality-Selection (MS) strategy to improve the performance of alignment. Finally, a two-stream feature alignment detector (TSFADet) based on the TSRA module is constructed for RGB-IR object detection in aerial images. With comprehensive experiments on the public DroneVehicle datasets, we verify that our method reduces the effect of the cross-modal misalignment and achieve robust detection results.