With increasing amount of attention being paid to single case randomized controlled trial (N-of-1 trials), sample size estimation has become an important issue for clinical researchers. This paper mainly introduces the model and hypothesis of N-of-1 trials. Based on the hypothetical model, sample size estimation methods of fixed model and random model are proposed. The premises of the model application, formulas and examples are then given. It is expected in case of conduction N-of-1 trials, the correct methods are used to estimate sample size and improve the research quality of N-of-1 trials.