In this article, the flutter vibrations of fluid-conveying thin-walled nanotubes subjected to magnetic field is investigated. For modeling fluid structure interaction, the nonlocal strain gradient thin-walled Timoshenko beam model, Knudsen number and magnetic nanoflow are assumed. The Knudsen number is considered to analyze the slip boundary conditions between the fluid-flow and the nanotube's wall, and the average velocity correction parameter is utilized to earn the modified flow velocity of nano-flow. Based on the extended Hamilton's principle, the size-dependent governing equations and associated boundary conditions are derived. The coupled equations of motion are transformed to a general eigenvalue problem by applying extended Galerkin technique under the cantilever end conditions. The influences of nonlocal parameter, strain gradient length scale, magnetic nanoflow, longitudinal magnetic field, Knudsen number on the eigenvalues and critical flutter velocity of the nanotubes are studied. (C) 2019 Elsevier Inc. All rights reserved.