Visual odometry and Simultaneous Localization And Mapping (SLAM) has been studied as one of the most important tasks in the areas of computer vision and robotics, to contribute to autonomous navigation and augmented reality systems. In case of feature-based odometry/SLAM, a moving visual sensor observes a set of 3D points from different viewpoints, correspondences between the projected 2D points in each image are usually established by feature tracking and matching. However, since the corresponding point could be erroneous and noisy, reliable uncertainty estimation can improve the accuracy of odometry/SLAM methods. In addition, inertial measurement unit is utilized to aid the visual sensor in terms of Visual-Inertial fusion. In this paper, we propose a method to estimate the uncertainty of feature correspondence using an inertial guidance robust to image degradation caused by motion blur, illumination change and occlusion. Modeling a guidance distribution to sample possible correspondence, we fit the distribution to an energy function based on image error, yielding more robust uncertainty than conventional methods. We also demonstrate the feasibility of our approach by incorporating it into one of recent visual-inertial odometry/SLAM algorithms for public datasets.