The analysis and mechanism of excessive long-term deflection of long-span prestressed concrete (PC) box girder bridges is concentrated recently. However, because of the lack of computing method, three dimensional (3D) analysis of PC continuous bridge especially including long-term shear lag effect is hard to analyze. According to this, a 3D creep analysis method for long-span PC bridges is illustrated in this paper first. The shear lag analysis of loads, prestress and their combination effect is carried out respectively. Based on this, the effect of shear lag to the long-term deflection of mid-span and whole-shape of the bridge is demonstrated. At the end, the different of computing between analysis with or without considering shear lag is discussed and some suggestion is proposed.