Baseflow is an important part of the evaluation of groundwater resources, the baseflow calculation has been a fundamental problem of hydrology. Using the 1958-1988 and 2006-2014 years of daily runoff data of Qilinzui Hydrological Station on the downstream of Zengjiang River, according to the advantages and disadvantages of various methods of baseflow separation, and Zengjiang’s hydrogeological conditions and runoff variation characteristics, first Kalinin trial method was used to calculate the baseflow of this region, and the effects of subjective factors on the baseflow calculation result in the application of this method was studied in depth. The results showed that the parameter selection was very important for the Kalinin trial method on the baseflow segmentation. Assuming that the selection of recession coefficient was in line with uniform distribution, the corresponding coefficient scale factor B obtained by the recession coefficient would not be uniformly distributed. Baseflow was calculated based on the two parameters. Without considering the influence of subjective factors, the multi-year baseflow of Zengjiang River had an average of 7.8 billion cubic meters for many years. Under the influence of subjective factors, the 95% confidence interval was 6.68-8.72 billion cubic. The direct calculation result was within this confidence interval, and the corresponding assurance rate was 41%. Therefore, considering the subjective uncertainty in baseflow calculation could not only be used to check the calculation results, but also put forward the reliability of the calculation results at the same time, which will provide important basis for decision making of groundwater resources management.