Abstract: Coulomb crystals have applications in many areas such as quantum computing and simulation, quantum logic spectroscopy, nonlinear dynamics and chaos, phase transitions, and chemical reaction process. The structure of the Coulomb crystal and the trajectory of each trapped ion are typically determined by the parameters of the trap and the ion species. However, dark ions are often inevitable in experiment, which introduces uncertainty into the desired crystal structures and ion trajectories. Few researches have been conducted to investigate the configuration change of the crystal in the presence of dark ions and the influence of a dark ion on its surrounding ion trajectories in a multi-ion system. In this work, we utilize the molecular dynamics simulation software LAMMPS and the (py)LIon package (modified to adapt the semi-classical theory of laser cooling) for simulating the three-dimensional ion trajectories of Coulomb crystals. The formation process of ⁴⁰Ca⁺ Coulomb crystal in a linear trap is simulated. With the micromotion and secular motion trajectories of each ion, we calculate the temperature of Coulomb crystal and the average velocity of specific ions. It is observed that the crystal structure exhibits obvious layering phenomenon when the trapped ions yield a large difference in their charge-to-mass ratio (CMR), however, layering is not obvious with a small difference in the CMR. In addition, we simulate and compare the Coulomb crystal structure formed by pure ⁴⁰Ca⁺ ions with that formed by ⁴⁰Ca⁺ ions mixed with a small number of dark ions including isotopic ions (⁴⁴Ca⁺) and impurity ions (CaH⁺). Three different cases are investigated, namely the one-dimensional ion string, two-dimensional planar structure and three-dimensional helical structure. The results show that the ions in the neighborhood of a dark ion exhibit around micron-order position change compared with their positions before the dark ion is formed. Such a change can be measured in experiment through microscopic imaging, thereby providing a way to identify the formation of dark ions in Column crystals with a large ion number.