Recently, nitrogen-doped carbon encapsulating with transition metal hybrids has attracted extensive interests in catalysis because of its unique microstructure and promising properties. In this work, three dimensional N-doped graphene-CNT frameworks with well encapsulated ultrafine Ni nanoparticles (Ni@N-CNTs/N-G) were developed by a facile two-stage encapsulation strategy by combining Ni-MOFs with melamine as the precursor. In terms of Cr(VI) reduction by using formic acid (HCOOH) as the reductant, N-CNTs/N-G matrix not only protected the encapsulated Ni nanoparticles from poisoning or leaching in strong acid media, but also provided enhanced active sites for Cr(VI) by its rich mesopores and high N content. Among all the products obtained after thermal treatments at different temperatures, Ni@N-CNTs/N-G-800 (pyrolyzed at 800 °C) exhibited superb reduction performance with the efficiency of approximately 99.6%, ascribing to the synergistic effects including the porous 3D framework with large specific surface area, high N-doping level, and large amount of ultrafine Ni nanoparticles. More importantly, its catalytic activity and microstructure rarely changed after 10 times of recycling, suggesting that Ni@N-CNTs/N-G-800 processes excellent stability. This study provides a new strategy of synthesizing transition metal-based catalyst, which can broaden the applicability of MOF materials for heavy metal pollution cleanup.