Tunable electronic properties upon doping make laboratory-grown nanodiamond films a promising and intriguing platform for not only refining conventional electronics, but also developing superconducting quantum devices. In a variety of superconducting systems, mostly in layered materials and heterointerfaces, superconductivity exhibits a two-dimensional (2D) character as evidenced by the anisotropy factor ε=μ0H∥c2/μ0H⊥c2≫1, where μ0H∥c2 and μ0H⊥c2 are the in-plane and out-of-plane upper critical fields, respectively. Here, we report on the observation of an anomalous anisotropy of superconductivity in heavily boron-doped nanodiamond films, which had been considered a purely three-dimensional (3D) material owing to the minute value of its coherence length in contrast to the film thickness. We investigate the resistive superconducting transition as a function of the angle of the applied magnetic field. The angular dependence of the resistive superconducting transition reveals ɛ < 1 in the nanodiamond films, indicating an anomalous anisotropy of the superconductivity. Our structural analysis shows that the grain boundaries, particularly twin boundaries, divide the nanodiamond film into nanoscale fragments standing out of the plane. The counterintuitive anisotropic superconductivity is interpreted as a result of the quantum confinement of the superconducting order parameter in the presence of the columnar grain boundaries and intragrain twin boundaries. This research provides physical insight for developing nanodiamond-based miniaturized superconducting quantum devices by making use of the as-grown grain boundaries and/or twin boundaries.