The nonlocal strain gradient theory, when combined with the first-order shear deformation theory, provides many capabilities in size-dependent structures. The aim of the present study is evaluation of the free vibration behavior of two vertically aligned fluid-conveying single-walled boron nitride nanotubes in hygrothermal environments considering slip boundary condition based on Knudsen number. These two adjacent nanotubes are coupled in the context of linear deformation through van der Waals interaction according to Lennard–Jones potential function. Actually, the contribution of the present work, compared with those previously reported, is investigating the simultaneous effect of hygrothermal loading and slip boundary condition on the dynamic behavior of two vertically aligned fluid-conveying single-walled boron nitride nanotubes. As an additional step to achieve a more accurate model of low-scale structures, both hardening and softening effects of materials are taken as important variables in the nonlocal strain gradient approach. To derive the motion equations and associated boundary conditions, Hamilton’s variational principle is used. The equations are then solved with the aid of differential quadrature method. Numerical studies are also performed to depict the effects of a number of parameters such as boundary conditions, size scale, aspect ratio, inter-tube distance, and temperature alteration on the variations of dimensionless eigenfrequency and critical flow velocity.