We report the facile and easy synthesis process of iron oxide (Fe3O4) nanoparticles (Fe3O4 NPs) modified surface of carbon nanotubes (CNTs) and their magnetic properties. The partially aligned multi-walled carbon nanotubes (MWCNTs) and nitrogen-doped multi-walled carbon nanotubes (CNx-MWCNTs) were synthesized through chemical vapor deposition (CVD) method. In next step, synthesized MWCNTs and CNx-MWCNTs were anchored with Fe3O4 NPs using microwave (MW) irradiation. The size of anchored Fe3O4 NPs on surface of Fe@MWCNTs and Fe@CNx-MWCNTs were 5–15 and 5–10 nm, respectively. The investigation results of magnetic properties revealed that the saturation magnetization of Fe@CNx-MWCNTs was improved after N-doping and Fe@CNx-MWCNTs showed superior magnetization behaviour than Fe@MWCNTs. The saturation magnetization value increases from 26.1 to 30.4 emu/g after N-doping. The improved magnetic performance of Fe@CNx-MWCNTs may be due to the induced structural defect on the surfaces which supports Fe3O4 NPs to attach and consequently improves the saturation magnetization.