Large-scale projects play an important role in social and economic development. Recently, large-scale projects are becoming more complex with more uncertainties and risks during the construction, which leads to more complex and extensive management problems. In a large-scale project, there is a principal-agent relationship between the contractor and owner. The contractor may take moral hazard behavior to pursue his/her own interests due to the information asymmetry and conflict of interest, which could damage to the public and owner’s interests. Based on the principal-agent theory, a dynamic incentive model combining explicit and implicit incentives was constructed in large-scale projects, after analyzing the mechanism of reputation effects. A comparison was made between two scenarios. One scenario considered reputation effects; the other did not consider reputation effects. The results show that the contractor would be more inclined to make optimal efforts in the large-scale project after reputation effects are introduced, and this optimal effort level will improve with the increased influence degree of reputation effects. However, the contractor’s degree of risk aversion will weaken the incentive effects. In addition, compared to an explicit incentive, the reputation mechanism of an implicit incentive will increase the owner’s benefits. The findings not only provide important support for the owner to formulate relevant incentive clauses in the construction contract, but also has important practical significance for the construction of the micro-institutional environment in construction projects. This study did not take into account factors such as regulatory efficiency when establishing the reputation incentive model. How to combine reputational incentives with the degree of supervision will be the direction of future research.