A novel magnetic responsive Ni-based metal–organic framework material was developed to efficiently separate and immobilize thermal enzymes with high catalytic performance. Ni-based metal–organic framework nanorods (Fe₃O₄/Ni-BTC) with high magnetic responsiveness are prepared conveniently by a one-pot hydrothermal process. With the characterization, it was confirmed that Ni-based metal–organic framework nanocomposites were synthesized as nanorods mounted with magnetic Fe₃O₄ nanoparticles on the surface. Although Fe₃O₄/Ni-BTC showed a preference for histidine-tagged enhanced green fluorescent protein (His-eGFP), we found that a variety of forces played roles in enzyme immobilization, including affinity between Ni²⁺ and histidine tags, electrostatic attraction, hydrogen bonding and hydrophobic forces. After understanding the mechanism of the as-prepared nanocomposites, a new immobilization strategy for thermostable S-adenosylmethionine synthetase (SAMS) was further evaluated. As a result, SAMS from cell lysate achieved about 95% activity recovery in the biosynthesis of S-adenosylmethionine (SAM) under high temperature conditions (70 °C) with a simple mixing step. At the same time, the immobilized enzyme was more stable against temperature variation (by nearly 8-fold in an 80 °C water bath after 2 h) and extreme pH (by nearly 1.3-fold at pH 3) and exhibited excellent reusability after immobilization. This work indicates that magnetic responsive Ni-based nanorods are highly promising for thermostable enzyme immobilization with high efficiency and stability.