The Community Land Model (CLM) is an advanced process-based land surface model that simulates carbon, nitrogen, water vapor and energy exchanges between terrestrial ecosystems and the atmosphere at various spatial and temporal scales. We use observed carbon and water fluxes from five representative Chinese Terrestrial Ecosystem Flux Research Network (ChinaFLUX) eddy covariance tower sites to systematically evaluate the new version CLM4.5 and old version CLM4.0, and to generate insights that may inform future model developments. CLM4.5 underestimates the annual carbon sink at three forest sites and one alpine grassland site but overestimates the carbon sink of a semi-arid grassland site. The annual carbon sink underestimation for the deciduous-dominated forest site results from underestimated daytime carbon sequestration during summer and overestimated nighttime carbon emission during spring and autumn. Compared to CLM4.0, the bias of annual gross primary production (GPP) is reduced by 24% and 28% in CLM4.5 at two subtropical forest sites. However, CLM4.5 still presents a large positive bias in annual GPP. The improvement in net ecosystem exchange (NEE) is limited, although soil respiration bias decreases by 16%–43% at three forest sites. CLM4.5 simulates lower soil water content in the dry season than CLM4.0 at two grassland sites. Drier soils produce a significant drop in the leaf area index and in GPP and an increase in respiration for CLM4.5. The new fire parameterization approach in CLM4.5 causes excessive burning at the Changbaishan forest site, resulting in an unexpected underestimation of NEE, vegetation carbon, and soil organic carbon by 46%, 95%, and 87%, respectively. Overall, our study reveals significant improvements achieved by CLM4.5 compared to CLM4.0, and suggests further developments on the parameterization of seasonal GPP and respiration, which will require a more effective representation of seasonal water conditions and the partitioning of net radiation between sensible and heat fluxes.