Abstract: The influence of different data processing methods on the fitting values of linear square(LQ) model parameters and the calculated values of biological dose distribution used in treatment planning were investigated in the cell cloning survival experiment. Four sets of LET-α and LET-β data were obtained based on the LQ model fitted to the data from the clonogenic survival experiments of carbon ion irradiated cells from T98G cells, according to whether the standard deviation of the cell survival rate was taken into account, and the plating efficiency was taken into account in two different ways, respectively, and three of them were selected to build the basedata of three datasets of the matRad treatment planning system for the treatment planning study. When only the 0 Gy plating efficiency was considered, whether the fitting considered the standard deviation of survival rate had little influence on the α value when the LET was low, but had a greater influence on the β value; With the LET getting larger, it had a greater impact on the α value and a lesser impact on the β value. When considering the standard deviation of survival rate, the deviations of fitting results in 2 different ways to consider the plating efficiency were small. Except for 200 keV/μm, the relative deviation of α values between the two groups did not exceed ±10%. Planset2 always overestimated D_max, D_min and D₉₅ compared to Planset1. The results illustrate that whether the standard deviation of survival rate were considered or not had a greater influence on the fitted α, β coefficients than considering the plating efficiency in 2 different ways. The relative deviation range of biological dose distribution’s calculation values among different datasets in the treatment planning system was smaller than the relative deviation range of α and β values of each group obtained by fitting the experimental data.