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.
Magwi County is partitioned into three sub-regions (Sudan): Magwi Sub-region, Pajok Sub-region, and Iwire Sub-region. The town of Magwi acts as the county's administrative center.