Abstract. Stand-replacing disturbances including harvests have substantial impacts on forest carbon (C) fluxes and stocks. The quantification and simulation of these effects is essential for better understanding forest C dynamics and informing forest management in the context of global change. We evaluated the process-based forest ecosystem model, PnET-CN, for how well and by what mechanisms changes of ecosystem C fluxes, aboveground C stocks (AGC), and leaf area index (LAI) arise after clearcuts. We compared the effects of stand-replacing harvesting on C fluxes and stocks using 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 values of normalized root mean square error (NRMSE) and the Willmott index of agreement (d) between simulated and inferred from observation variables including gross primary productivity (GPP), ecosystem respiration (ER), net ecosystem productivity (NEP), LAI, and AGC in the two chronosequences were 20% and 0.90, respectively. Simulated 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 ER for both forest types was initially as high as ∼700–1000 g C m−2 yr−1 in the first or second year after clearcuts, 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 NEP for both forest types was initially negative with the net C losses of ∼400–700 g C m−2 yr−1 for 6–17 years after harvesting, reached the peak values of ∼400–600 g C m−2 yr−1 at 14–29 years of age, and became stable and a weak C sink (∼100–200 g C m−2 yr−1) in mature forests (>60 years old). The decline of NEP with age was caused by the relative flatting of GPP and gradual increasing of ER. ENF recovered slower from net C source to net sink and lost more C than DBF, suggesting ENF are likely slower to recover C assimilation capacity after stand-replacing harvests due to slower development of photosynthesis with stand age. Model results indicated that increasing harvesting intensity would delay recovery of NEP after clearing, but had little effect on C dynamics during late succession. Further improvements in numerical process-based forest population dynamic models for predicting the effects of climate change and forest harvests are considered.