Carbon compensation can guide human activities in reducing carbon emissions or increasing carbon sequestration and also represents an important approach for coordinating regional development. In this paper, Chongqing Municipality, whose internal development is varied, was selected as a case study. The annual carbon emissions, carbon sequestration, carbon deficits, and inter-regional carbon compensation costs from 2000 to 2021 were continuously estimated via local optimization methods, and a carbon compensation zoning scheme was proposed that integrates the present situation and trend analysis. The results show that (1) Chongqing’s total carbon emissions were greater than the total carbon sequestration, and the carbon deficit was approximately 556.24 × 104 t~3621.58 × 104 t. (2) County-level carbon budgets have large regional differences; the counties that should always receive carbon compensation are from the southeast and northeast regions, and the counties that should always pay carbon compensation are from central urban areas and the surrounding new urban areas. (3) All the counties were zoned into key payment areas, basic payment areas, key recipient areas, and basic recipient areas. The key payment areas, which account for 39.47%, maintain and grow payment status and are the main sources of carbon compensation costs, while the key recipient areas, which account for 44.74%, maintained a negative compensation status and a continuous downward trend, meaning that they may receive increasing carbon compensation costs. This paper revealed inequities in carbon compensation and proposed a novel zoning solution, which can provide scientific reference and data support for further establishing inter-regional carbon compensation mechanisms.