Flood disaster is one of the natural disasters which cause the most serious economic losses, the most casualties, and the greatest social impact. Flood frequency analysis is very important for reducing flood disaster. In this paper, based on the flood data of Manas River and tools of Box–Cox and Johnson normal transformation, the nonparametric statistical method for flood frequency analysis is studied in order to analyze the adaptability between it and the rivers in arid region of north-western China. The calculation result of the fitness index is divided into two parts: high flood discharge and low flood discharge. One of the two evaluation indexes has an advantage in fitting, and the number of advantages of the three methods in each part has been counted. After analysis, for the flood peak discharge frequency of rivers in arid region of north-western China, the frequency curve of Johnson transformation fits best with empirical data. The high flood discharge advantage is 6, and the low flood discharge is 4. For the flood volume frequency of rivers in arid region of north-western China, Box–Cox transform fits well with empirical data at the high flood discharge frequency curve, and its advantage is 12; Johnson transformation has a better fit between the low flood discharge frequency curve and empirical data, and its advantage is 12. Therefore, it is the way of improving the precision of flood frequency analysis to use the method of P-III distribution and normal transformation comprehensively.