Climate warming increases carbon assimilation by plant growth and also accelerates permafrost CO₂ emissions; however, the overall ecosystem CO₂ balance in permafrost regions and its economic impacts remain largely unknown. Here we synthesize in situ measurements of net ecosystem CO₂ exchange to assess current and future carbon budgets across the northern permafrost regions using the random forest model and calculate their economic implications under the Shared Socio-economic Pathways (SSPs) based on the PAGE-ICE model. We estimate a contemporary CO₂ emission of 1,539 Tg C during the nongrowing season and CO₂ uptake of 2,330 Tg C during the growing season, respectively. Air temperature and precipitation exert the most control over the net ecosystem exchange in the nongrowing season, while leaf area index plays a more important role in the growing season. This region will probably shift to a carbon source after 2,057 under SSP5-8.5, with a net emission of 17 Pg C during 2057–2100. The net economic benefits of CO₂ budget will be $4.5, $5.0, and $2.9 trillion under SSP1-2.6, SSP2-4.5, and SSP5-8.5, respectively. Our results imply that a high-emission pathway will greatly reduce the economic benefit of carbon assimilation in northern permafrost regions.