The Improving Connectivity in the Central Forest Spine (IC-CFS) is funded by the Malaysian Government (GOM) and the Global Environment Facility (GEF). The IC-CFS main objective is to re-establish, maintain, and improve the connectivity within the corridors and create linkages between the fragmented forests. The carbon stock assessment component is required to evaluate the corridors. The study was conducted at Primary Linkages in Pahang (C-PL1), A-PL1 in Perak, and J-PL2 in Johor, with an extent of 4,355 ha, 24,759 ha, and with 6,791 ha, respectively. The Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) tool was applied for assessing the carbon stock within these landscapes together with satellite images between the years 2010 and 2020 to produce land use classifications. Carbon stock in J-PL2 indicated depletion by -592,599 Mg C over ten years. On the other hand, C-PL1 and A-PL1 indicated an increase amounted 22,129 and 695,689 Mg C, respectively. These changes evidenced that the land use activities were influenced directly and significantly by the fluctuations of carbon stock, i.e., absorption and emission within the corridors. Conclusively, the InVEST tool is practical for carbon assessment, management, and conservation planning to ensure the connectivity and sustainability of CFS corridors in Peninsular Malaysia.