Objective To evaluate the procedures for patient-specific quality assurance ( QA ) measurements using modulated spot scanning beam for proton and carbon ion treatment. Methods Records of 1734 beam measurements were analyzed by using a passing criteria, namely, dose difference between the measured and calculated doses≤3% or distance-to-agreement ( DTA) between them≤3 mm, and meanwhile mean dose deviation in all chambers ≤3% and at least 22 of 24 chamber array having passed this criteria. The results of measurement were categoried by water phantom, treatment room, measurement depth in chamber array, etc. Results Stratification of result showed some correlation between measurement parameters and passing rates. The total passing rates were 97. 7% and 91. 9% for proton and carbon ion beams, respectively. The passing rates were high at all measurement depths for proton beam, but decreased for carbon ion beam with increased depth. Chambers were mostly stable, leading to no significant difference in passing rate between different water phantoms and between different treatment rooms. Conclusions A good agreement was shown between the doses measured by water phantoms with those by the treatment planning system ( TPS) . When the chamber position was deeper than 150 mm in carbon ion measurements, a lower passing rate was observed. This could be caused by uncertainty of ion chamber array setup ( lateral and in depth) in highly modulated beams or by incorrect modelling of scattering by the TPS. These deviations need the further investigation.