Y. D. Tunnel, designed with a speed of 200 km and doubleblock ballastless track, in Southwest China is about 7.85 km in length. Varying degrees of heaving appeared in the floor structure of the tunnel within the region of K107+970～K109+270 after it was put into service. Cracks and failure developed in the ballastless tracks, resulting in track geometry changing in an unstable state. The railway operation was seriously influenced. The tunnel was located in lowmedium thick interbedded strata of mediumweathered mudstone and sandstone. The insitu stress was measured, indicating that there existed high horizontal stress nearly perpendicular to the tunnel axis. In the paper, the causes for the heaving of the floor structure of the tunnel are analyzed by means of field survey and measurement, theoretical analysis and numerical simulation. It is concluded that the causes for the heaving of the floor structure are as follows: 1) Superhigh ground stress, mainly taking the form of horizontal structural stress, acts on the slightlydipping interbedded lowmedium thick rock mass underlying the tunnel floor; 2) The parameters of the invert cannot meet the requirements of the geological conditions. The following countermeasures are proposed for the treatment of the floor heaving: 1) For tunnels located in slightlydipping interbedded rock mass and under 50 m～300 m cover, special attention should be paid to the specific design of the floor and appropriate rise span ratio and rigidity should be selected for the tunnel invert; 2) Due to the loosening and sliding features of the anchor cables, the anchor cables cannot be taken as the only or major technological measures to control the heaving of the tunnel floor; on the other hand, rock bolting, at least “rigid control measures + flexible control measures” should be taken to control the heaving of the tunnel floor.