Magwi County is divided into three payams (Sudan)|payams (sub-counties): Magwi Payam, Pajok Payam and Iwire Payam. The town of Magwi is the county headquarters.
The administrative area of Magwi County comprises three local districts: Magwi District, Pajok District, and Iwire District. The town of Magwi functions as the county's central location.