Habitat manipulation is an important technique that can be used for controlling rodent damage in agricultural ecosystems. It involves intentional manipulation of vegetation cover in habitats adjacent to active burrows of rodents to reduce shelter and food availability and to increase predation pressure. The current study was conducted in the Pothwar Plateau region of Pakistan during respective non-crop periods of wheat-groundnut (post-harvested and un-plowed/non-crop fallow lands). The purpose was to assess the impact of reduction in vegetation height of adjacent habitats (field borders) on rodent richness and abundance. The study area was divided into two sites: treated and non-treated. At the treated sites, habitat manipulation was carried out by removing crop cache and non-crop vegetation over 10 cm in height to a distance of approximately 20 m from the fields. The trapping sessions carried out at both treated and non-treated sites adjacent to wheat-groundnut fields were significantly different (F2,6 = 13.2, P = 0.001) from each other, with the maximum number of rodents captured from non-treated sites. There was a significant difference in the overall abundance of rodents (P < 0.05) between crop stages and between treatments in both crops. The manipulation effect was observed with respect to damage to crops and yield production, significantly reducing damage within the associated croplands (P < 0.05). The outcomes of this study indicated a significant reduction of rodent population at treated sites due to changes in vegetation height and cover, which directly affect habitat and behavior attributes (e.g., food, shelter, movements, increased risk sensitivity, and feeding behavior) for rat. Rodents apparently were unable to reach levels where they could cause significant crop damage. This method is recommended as a cost-effective and easy application.