Objective:To assess proton biological dose with using two kinds of relative biological effect models and to compare them with traditional clinical proton biological dose ( Dose1.1). Methods:Based on Particle simulation tools(TOPAS), physical dose, LET d and LET t were calculated in water phantom and two anthropomorphic phantoms (brain and prostate tumors) respectively. Then DoseLET d and DoseLET t were calculated according to different relative biological effect models, an RBE was 1.1 in traditional clinical proton biological dose calculation. Three kinds of biological doses were compared in the water phantom. To quantify the differences between three method in anthropomorphic phantoms, three points ( D1, D2, D3) were selected according to the physical dose to compare the biological dose. Results:DoseLET d and DoseLET t in water phantom showed the same trend with water depth and both of them were higher than Dose1.1 at the end of proton beam range. The maximal difference between DoseLET d and DoseLET t in the anthropomorphic phantoms was 10.08 cGy, where the relative difference was less than 5%. When DoseLET d and DoseLET t were compared with Dose1.1, the maximal differences in brain tumor target were 71.97 cGy and 61.91 cGy respectively, where the relative differences were less than 25%. The maximal differences in prostate tumor target were 25.95 and 19.96 cGy respectively, where the relative differences were less than 12%. However, the differences outside the target were very small, where the maximal differences in brain and prostate tumors were 5.99 cGy and 9.92 cGy respectively, and the relative differences were less than 5%. Conclusions:Biological doses calculated by two method are of little difference in both water and anthropomorphic phantoms, however, large differences were observed when they were compared with the traditional clinical proton biological dose especially in the high dose area.