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The intercomparison of Moderate Resolution Imaging Spectroradiometer (MODIS) reflective solar bands onboard Aqua and Terra is very important for the assessment of each instrument’s calibration. One of the limitations is the lack of simultaneous nadir overpasses. Their measurements over a selected Earth view target have significant differences in solar and view angles, which magnify the effects of atmospheric scattering and bidirectional reflectance distribution function (BRDF). In this paper, an intercomparison technique is formulated after correction for site’s BRDF and atmospheric effects. The reflectance measurements over Libya desert sites 1, 2, and 4 from both the Aqua and Terra MODIS are regressed to a BRDF model with an adjustable coefficient accounting for calibration difference. The ratio between Aqua and Terra reflectance measurements is derived for bands 1-9 and the results from different sites show good agreement. For year 2003, the ratios are in the range of 0.985-1.010 for bands 1-9. Band 3 shows the lowest ratio 0.985 and band 1 shows the highest ratio 1.010. For the year 2014, the ratio ranges from approximately 0.983 for bands 2 and 1.012 for band 8. The BRDF corrected reflectance for the two instruments is also derived for every year from 2003 to 2014 for stability assessment. Bands 1 and 2 show greater than 1% differences between the two instruments. Aqua bands 1 and 2 show downward trends while Terra bands 1 and 2 show upward trends. Bands 8 and 9 of both Aqua and Terra show large variations of reflectance measurement over time.