Lonsdaleite is a carbon allotrope and metastable form of diamond that demonstrates superior mechanical properties over cubic diamond. Here, we report the results of density functional theory (DFT) and molecular dynamics (MD) study of neutral and negative nitrogen vacancy center in lonsdaleite. Interestingly, neutral (NV0) and negative (NV-1) nitrogen-vacancy center in lonsdaleite display a remarkable splitting in the two degenerate ex and ey excited states nearly around ~ 0.5 eV for NV0 and 0.2 eV for NV-1. The thermal stability, dynamic stability, band structure, density of states, and optical properties are computed. The DFT and MD calculations reveal that geometrical structure of NV center in lonsdaleite is both thermally and dynamically stable. In addition, the findings show that NV0 and NV-1centers in lonsdaleite demonstrate splitting in the zero-phonon line (ZPL) due to symmetry reduction from C3v to C1h with respect to NV center in cubic diamond. Furthermore, the results indicate that ZPL falls around ~ 1.76 and 2.25 eV for NV0, while it lies around 1.91 and 2.19 eV for NV-1.