The article presents the synthesis, structural and magnetic properties of NixNbSe2 (x = 0, 0.05, 0.1, 0.15, 0.2, 0.25). The intercalation limit of Ni in NbSe2 is found to be 25 mol%, above which NiSe appears as a binary impurity phase. Single crystal X-ray diffraction studies show that all the compounds crystallize in the hexagonal P63/mmc space group. However, there is a distinct phase transition beyond x = 0.20 with Ni intercalation in NixNbSe2. The NixNbSe2 compounds crystallized in the parent 2H phase with x value between 0 ≤ x ≤ 0.2. Subsequently, the phase transforms into the 2H(I) phase with an order superstructure of 2 ao × 2 ao × 1 co for 0.20 ≤ x ≤ 0.25 in NixNbSe2. The superstructure formation is attributed to the occupation of Ni at the alternate octahedral voids present in the van der Waals gap of the NbSe2. The XPS results and theoretical analysis clearly show that the intercalation of Ni results in a more metallic character in NixNbSe2. Magnetic measurements on NixNbSe2 (x = 0.05, 0.1, 0.2, 0.25) shows very small magnetic moment at low temperature for all the compounds. Theoretical calculation on Ni0.25NbSe2 shows that the Ni-3d electrons are delocalized and are very weakly spin-polarized, which may be the reason for the experimentally observed weak magnetism in these compounds.