Magnetic skyrmion, i.e. a topologically stable swirling spin texture, appears as a particle-like object in the two-dimensional (2D) systems, and has recently attracted attention as a candidate of novel information carrier. In the real three-dimensional (3D) systems, a skyrmion is expected to form a string structure along an extra dimension, while its experimental identification has rarely been achieved. Here, we report the direct visualization of 3D shape of individual skyrmion strings, for the recently discovered room-temperature skyrmion-hosting noncentrosymmetric compound Mn1.4Pt0.9Pd0.1Sn. For this purpose, we have newly developed the magnetic X-ray tomography measurement system that can apply magnetic field, which plays a key role on the present achievement. Through the tomographic reconstruction of the 3D magnetization distribution based on the transmission images taken from various angles, a genuine skyrmion string running through the entire thickness of the sample, as well as various defect structures such as the interrupted and Y-shaped strings, are successfully identified. The observed point defect may represent the emergent magnetic monopole, as recently proposed theoretically. The present tomographic approach with tunable magnetic field paves the way for the direct visualization of the structural dynamics of individual skyrmion strings in the 3D space, which will contribute to the better understanding of the creation, annihilation and transfer process of these topological objects toward the potential device applications.