Harvest disturbance has substantial impacts on forest carbon (C) fluxes and stocks. The quantification of these effects is essential for the better understanding of forest C dynamics and informing forest management in the context of global change. We used a process-based forest ecosystem model, PnET-CN, to evaluate how, and by what mechanisms, clear-cuts alter ecosystem C fluxes, aboveground C stocks (AGC), and leaf area index (LAI) in northern temperate forests. We compared C fluxes and stocks predicted by the model and observed at two chronosequences of eddy covariance flux sites for deciduous broadleaf forests (DBF) and evergreen needleleaf forests (ENF) in the Upper Midwest region of northern Wisconsin and Michigan, USA. The average normalized root mean square error (NRMSE) and the Willmott index of agreement (<i>d</i>) for carbon fluxes, LAI, and AGC in the two chronosequences were 20% and 0.90, respectively. Simulated gross primary productivity (GPP) increased with stand age, reaching a maximum (1200–1500 g C m⁻² yr⁻¹) at 11–30 years of age, and leveled off thereafter (900–1000 g C m⁻² yr⁻¹). Simulated ecosystem respiration (ER) for both plant functional types (PFTs) was initially as high as 700–1000 g C m⁻² yr⁻¹ in the first or second year after harvesting, decreased with age (400–800 g C m⁻² yr⁻¹) before canopy closure at 10–25 years of age, and increased to 800–900 g C m⁻² yr⁻¹ with stand development after canopy recovery. Simulated net ecosystem productivity (NEP) for both PFTs was initially negative, with net C losses of 400–700 g C m⁻² yr⁻¹ for 6–17 years after clear-cuts, reaching peak values of 400–600 g C m⁻² yr⁻¹ at 14–29 years of age, and eventually stabilizing in mature forests (> 60 years old), with a weak C sink (100–200 g C m⁻² yr⁻¹). The decline of NEP with age was caused by the relative flattening of GPP and gradual increase of ER. ENF recovered more slowly from a net C source to a net sink, and lost more C than DBF. This suggests that in general ENF may be slower to recover to full C assimilation capacity after stand-replacing harvests, arising from the slower development of photosynthesis with stand age. Our model results indicated that increased harvesting intensity would delay the recovery of NEP after clear-cuts, but this had little effect on C dynamics during late succession. Future modeling studies of disturbance effects will benefit from the incorporation of forest population dynamics (e.g., regeneration and mortality) and relationships between age-related model parameters and state variables (e.g., LAI) into the model.