Preference relations are very useful to express decision makers' preferences over alternatives in the process of group decision-making. However, the multiple self-confidence levels are not considered in existing preference relations. In this study, we define the preference relation with self-confidence by taking multiple self-confidence levels into consideration, and we call it the preference relation with self-confidence. Furthermore, we present a two-stage linear programming model for estimating the collective preference vector for the group decision-making based on heterogeneous preference relations with self-confidence. Finally, numerical examples are used to illustrate the two-stage linear programming model, and a comparative analysis is carried out to show how self-confidence levels influence on the group decision-making results.