In the present work, a series of single phase Ni-doped skutterudite compounds NixCo4−xSb12 (x = 0.1, 0.2, 0.3, 0.4, 0.5) were successful synthesized by 5 min microwave heating for the first time. The resulting ingots was pulverized and sintered by spark plasma sintering to fabricate bulk samples, and their microstructure and thermoelectric properties have been investigated systematically. The results show that the matrix grain characteristics are influenced by Ni concentration and microwave irradiation. The Ni0.3Co3.7Sb12 bulk has the smallest and uniform grain size of about 1–2 µm. The maximum power factors of NixCo4−xSb12 are 2273, 2479, 2711, 2613 and 2526 µWm−1K−2 respectively. A highest ZT of 0.52 for Ni0.3Co3.7Sb12 is achieved at 773 K along with a total thermal conductivity of 3.8 Wm−1K−1.