Using 55 MeV/u40Ar and 80 MeV/u20Ne ion beams delivered by the Heavy Ion Research Facility at Lanzhou (HIRFL), the relationships between the irradiation homogeneities in irradiation fields generated by the beam scanning device located at the irradiation terminal of the HIRFL and ion fluence were measured respectively with 100 μm polycarbonate films by means of nuclear track detection. The results show that the homogeneity increases when the ion fluence are lower than 1×106 and 2×107 ions/cm2, and the homogeneity has a gradual increase at the fluence of 1×106-1×107 and 2×107-1×108 ions/cm2 and then reached about 58% and 61% when the fluence are higher than 1×107 and 1×108 ions/cm2, respectively, for the40Ar and20Ne ion beams. It is evident that the homogeneity in the irradiation field made by the beam scanning device presently cannot satisfy the requirements of researches such as heavyion induced biological effects, etc. Therefore, the performance of the scanning device should be improved further.