Keratoconus (KC) is a common degenerative corneal disease, and heredity plays a key role in its development. Although few genes are known to cause KC, a large proportion of disease-causing genes remain to be revealed. Here, we report the identification of TUBA3D as a novel gene linked to KC. Using whole-exome sequencing of a twins pedigree, a novel de novo mutation (c.31 C > T, p.Gln11stop) in TUBA3D gene was identified. A screening performed in 200 additional unrelated patients with KC revealed another two mutations (c.201insTT, p.Val68Leufs*2; c.*2 G > A) in two patients. TUBA3D was expressed highly in the cornea, and the twins had lower TUBA3D expression and higher UPA and MMP1 expressions than the normal parents. Through function prediction and in vitro cell experiment, we further demonstrated that the mutant proteins of TUBA3D were unstable and could lead to human corneal fibroblast cells performing higher MMPs expression and oxidative stress. These changes thus reduce the amount of extracellular matrices within corneas and undoubtedly play a major role in stromal thinning, which is characteristic of KC corneas. Our study showed that TUBA3D is a new gene that causes KC, thus supporting the evidence that this protein has an additional function into the human cornea.