Purpose: To demonstrate the improvement in IMRT patient specific quality assurance (QA) by considering a more accurate absolute dose calibration in MapCHECK, machine hardware characteristics and modification in beam modeling in treatment planning system (TPS). Method and Materials: MapCHECK, a 2D diode array system, was used in our routine IMRT patient specific QA on Elekta Synergy S LINAC with Beam Modulator (BM). To explore the absolute dose calibration in MapCHECK, dose at 10 cm water equivalent depth under same reference conditions was calculated for a 6 MV beam for both MapCHECK phantom (CT scanned MapCHECK with 8 cm solid water buildup) and a water phantom (50×50×50 cm3) by Pinnacle TPS, then was compared to each other. 2D dose measurements using film and MapCHECK for 4×4 and 16×16 cm2 were compared with water tank measurements to evaluate the field asymmetry. Results: (1) A 2% systematic difference has been detected in MapCHECK absolute dose calibration. If the QA plan is generated on a solid water phantom rather than on the scanned MapCHECK plus buildup, the pass‐rate can be improved by 1–2%. (2) Accounting for the asymmetric field in superior‐inferior direction associated with beam modulator design, a collimator rotation by 90 degrees in original patient IMRT plans can improve QA pass‐rate by up to 10%. (3) After reducing the source size in Pinnacle TPS beam model to better describe the penumbra, the pass‐rate increased several percent. Comparing QA results before and after implementing steps 1 through 3 in our clinical practice, the pass‐rate increased from 94.7%±2.5%(SD) to 98.6%±2.5%(SD) averaged over 28 patient QAs in each group. Conclusions: By correcting the systematic error in MapCHECK absolute dose calibration, rotating collimator by 90 degrees in patient plans and using a smaller source size in Pinnacle beam model, QA pass‐rate has been significantly improved.