The soybean pod borer, Leguminivora glycinivorella (Matsumura), is an important soybean pest that reduces both quality and yield in Asia, and chemical control is used irrespective of the damage risk. The pest population density increases at continuously cropped soybean fields (hereafter, source habitat). The present study would contribute to proposing pest management options matched to the damage risk by clarifying the surrounding landscape structures where damage is likely to increase. First, we clarified the relationship between the probability of grain damage and the source habitat within a 350 m radius of the new or continuously cropped soybean fields. The habitat area surrounding continuous soybean fields positively influenced the probability of grain damage but did not detect a significant effect in new soybean fields. Secondly, we clarified the relationship between the probability of grain damage and habitat connectivity in continuous soybean fields. Well-managed fields with high connectivity consistently showed low damage risk. Meanwhile, damage risk varied in fields with low connectivity, indicating that damage is unlikely to occur because soybean pod borers are difficult to invade. However, once invaded, the damage could be extensive. Considering these results, one possible new control system will allow the spatiotemporal variation in the number of insecticide applications. The present study likely contributes to understanding the relationship between soybean pod borer injury and landscape structure, which is important for area-wide pest management.