The uncertainty of intuitionistic fuzzy numbers (IFNs) is further enhanced by the existence of the degree of hesitation (DH). The shortcomings of existing researches are mainly reflected in the following situations: when comparing IFNs, the comparison rules of IFNs are difficult to apply to the comparison of any two IFNs, or the relevant methods do not fully consider the uncertainty expressed by DH. Thus, the rationality of the decision results needs to be improved. On the other hand, multi-attribute decision making (DADM) based on IFNs is often not objective due to the need to determine the attribute weight. Moreover, the strict condition of attribute aggregation of classical dominance relation makes it a method that fails considering the practical application. Aiming at the comparison problem of IFNs, this paper takes probability conversion as the starting point and proposes an IFN comparison method based on the area method, which can better deal with the comparison problem of “either superior or inferior” IFNs. In addition, aiming at the MADM problem of an intuitionistic fuzzy information system, we propose an intuitionistic fuzzy probabilistic dominance relation model and construct the MADM method under the probabilistic dominance relation. The series properties of IFNs and probabilistic dominance relation were summarized and proved, which theoretically ensured the scientificity and rigor of the method. The results show that the comparison and ranking method of IFNs proposed in this paper can be applied to the comparison of any two IFNs, and the dominance degree of IFNs is presented in the form of probability, which is more flexible and practical than the classical method. The probabilistic dominance relation method based on IFNs avoids the problem of determining attribute weights subjectively or objectively, and the decision maker can reflect decision preference by adjusting decision parameters to better match the actual problem. The application of this model to a campus express site evaluation further verifies the feasibility of the proposed method and the rationality of the results. In addition, various extension problems of the model and method proposed in this paper are discussed, which pave the way for future related research. This paper constructs a complete decision-making framework through theoretical analysis and application from practical problems, which provides a reference for enriching and improving uncertain decision-making theory and the MADM method.