In recent years some progress has been made about the addition of Carbon Nanotubes (CNTs) in the stainless steel metal matrix by pulsed Gas Tungsten Arc Welding (P-GTAW). Despite that, there is lack of information regarding to microstructural modifications induced by CNTs in dissimilar welding. In this sense, we present the welding of nanocomposite based on Nickel/Carbon Nanotubes-stainless steel 316L alloy (Ni/CNTs-SS 316L), as the welding metal, on carbon-manganese (C-Mn) non-alloyed structural steel, as the base metal. The microstructure of manufactured specimens with/without nanocomposite was characterized by: optical microscopy; Raman spectroscopy; scanning electron microscopy with energy dispersive spectroscopy (SEM-EDS) and electron backscattering diffraction (EBSD). Moreover, Vickers tests were performed from the welding metal (WM) to the base metal (BM) before/after temper treatment in order to investigate the microhardness changes. The results show that dilution rate and grain size for specimen with nanocomposite was higher than without nanocomposite; the CNTs affected the misorientation angle and texture of the WM; the topside microhardness from WM with Ni-CNTs was on average 30.40% higher than BM; and, in transverse cross-section microhardness was 31% higher than control sample on average at fusion line zone. These results indicate that addition of CNTs in the metallic matrix by dissimilar welding is a fertile ground for new studies applicable to manufacturing industry.