Floor heave is a typical tunnel issue in tunnelling engineering. To gain deep insights into the deformation mechanism and failure processes of floor heave at the bottom of a tunnel in layered rock, biaxial step-loading tests were conducted on rock samples (including schist and sandstone) with and without prefabricated invert arches. The failure processes of the samples were observed by the three-dimensional digital image correlation technique (3D-DIC) during the test. The test results showed that the deformation evolution processes of the floor heave of the sample included the following steps: (1) crack initiation at the interlayer weak planes; (2) separation of the rock matrix into platy structures along the bedding planes and flexures; and (3) fracture and uplift of the platy structures in the middle part. As the stress redistributes on the bottom plate of the sample, and stress concentration zones shift toward locations far away from the arching surface, the deformation evolution shows a similar variation trend with the stress. Continuous buckling fracturing takes place progressively from the vicinity of the arch surface to certain distant regions. Based on the test results, the key location of internal surrounding rock deformation was determined, and the mechanism of floor heave was clarified. The schist sample SC-BI-10 began to experience floor heave at 1064.4 s, and the deformation curve (the relationship between Y and U) showed a convex shape in the range of 0–20 mm in the Y-coordinate. The displacement reached its maximum value at y = 11.7 mm, corresponding to the position where the rock slab was broken. In addition, the influence of the interlayer properties and cover depth of rocks on bottom uplift was also studied. The design of tunnel supports and the monitoring and prevention of floor heave can benefit from this study.