This paper compares by land cover type seasonal and spatial variations of MODIS leaf area index (LAI) and fraction of photosynthetically active radiation (0.4–0.7 μm) absorbed by vegetation (FPAR) from 2.5 years with those from the Common Land Model (CLM) and investigates possible reasons for notable differences. The FPAR value is mainly determined by LAI in MODIS and both LAI and stem area index (SAI) in CLM. On average, the model underestimates FPAR in the Southern Hemisphere and overestimates FPAR over most areas in the Northern Hemisphere compared to MODIS observations during all seasons except northern middle latitude summer. Such overestimation is most significant in winter over northern high latitudes. The MODIS LAI is generally consistent with the model during the snow-free periods but may be underestimated in the presence of snow, especially for evergreen trees. The positive FPAR bias is mainly attributed to CLM SAI of deciduous canopy and higher LAI than MODIS for evergreen canopy as well. The negative FPAR bias results from several factors, including differences in LAI and soil albedo between CLM and MODIS or limitations of the geometric optics scheme used in the model. Therefore the MODIS algorithm needs to better represent the winter LAI retrievals, while the model needs to better quantify LAI and SAI. Since stems will not have the same single-scattering albedo as green leaves, it may be inappropriate for the model to treat LAI and SAI the same in the FPAR and albedo parameterizations. If so, the role of SAI in these parameterizations needs reformulation.