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Photosynthetically active radiation (PAR) is a key parameter for almost all terrestrial ecosystem models. However, the usefulness of the currently available PAR products is constricted by their limited spatial and temporal resolution. In this paper, the processes of PAR in Heihe River Basin are thoroughly studied by improved Eck and Dye model during the period 2000–2008. 8-day composite and annual PAR are calculated using TOMS (Total Ozone Mapping Spectrometer) and OMI (Ozone Monitoring Instrument) reflectance data during 9 years. The results indicate that that the changes of estimated PAR in study area are totally fluctuating over the past several years. Annual total PAR increases from upstream to downstream. Meanwhiles, four representative sites with different landscape types in study area are selected for analyzing seasonal dynamics and interannual variations. Further, because of the remotely sensed data with higher resolutions in 2005–2008, the discrepancies of total annual PAR between these study sites are more obvious over last 4 years.