The surrounding conditions of tunnel lining may change during the investment period which leads to a redistribution of forces acting on the tunnel lining and perhaps gives new forces are not taken into account during the design. The behavior of the tunnel should be analyzed for the new conditions and assess its performance through the stages of investment. In this paper, a case study of Alsafkon tunnel which is one of the Syrian Railway deep tunnels is regarded. The lining of this tunnel suffers from cracks, leakage, and other defects. To analyze the behavior of the tunnel lining, it has been modeled using the finite element method software Phase for five cases that represent the investment conditions experienced by the tunnel from its construction to date. It was found that the lining cracks appear from the third phase which represents the case of immersion of the tunnel by the underground water. The formation of a weak lens adjacent to the tunnel detected by geo radar plays also an important role in the cracking of the lining of the tunnel. The results of numerical analysis were in correspondence with the current situation of the tunnel in terms of distributed cracks places in the concrete lining. The study showed also the improvement importance of the lens properties to avoid the total fall down of the tunnel.