Stress is one of the most important physical indexes reflecting the mechanical behavior of concrete structures. In general, stress in structures cannot be directly monitored and can only be estimated through an established model of stress and strain. The accuracy of the estimated stress depends on the rationality of the established model for stress and strain. As the strain measured by sensors contains creep, shrinkage, and elastic strain, it is difficult to establish an analytical model for strain and stress. In this paper, a statistical inverse method was utilized to estimate the stress in continuously pre-stressed concrete beams based on the monitored strain. Stress in the beams and the model uncertainty factors were treated as model parameters. A linear-simplified method was adopted to determine the prior distribution of the stresses. The posterior distribution of the stresses at different locations during bridge construction can be obtained by the proposed method. A continuously pre-stressed concrete beam bridge was taken as the case study to verify the effectiveness of the proposed method. Additionally, the constitution of the total strain in the different construction stages was calculated. It was concluded that the creep strain is the dominant part of the total strain.