This paper devotes to predicting and analyzing the fluctuation of the thrust force during drilling of unidirectional carbon fiber reinforced plastics (UD-CFRPs). The fluctuation properties could be evaluated by the average value, maximum value, minimum value, change frequency and the amplitude of thrust force. Firstly, an orthogonal cutting model is introduced, and the model is modified in order to reveal how the drilling parameters affect the fluctuation. Secondly, the cutting lips are assumed to conduct orthogonal cutting, and the thrust force generated on cutting lips is calculated by using the orthogonal cutting model. Thirdly, the variable parameter, which leads to the fluctuation of thrust force, involved in the analytical model is analyzed separately. Lastly, experiments were conducted to determine the coefficients and testify the model. The comparison between the theoretical values and the experimental results prove that the analytical model can predict the fluctuation of thrust force well.