This article deals with a CO2 critical microchannel convective flow with heat applied from two side walls. Fluid near its gas–liquid critical point is very dense and much expandable; meanwhile, the thermal diffusivity tends to zero when it goes near the critical point. In microchannels, the effect of natural convection becomes negligible and the boundary thermal–mechanical effects will dominate the convection and thermal equilibrium processes. We numerically simulate the convection behaviours of near-critical fluids confined in microchannels by solving the Navier–Stokes equations together with conservative equations of mass and energy. Due to the thermal–mechanical effects of critical fluid, abnormal convection-onset structures and transient micro-scale vortex/mixing evolution modes have been found. The thermal–mechanical/acoustic perturbation source identified here contributes to a new type of Kelvin–Helmholtz instability when gravity is suppressed. The thermal–mechanical oscillations in the boundaries serve as the origin of current vortex phenomena from fast boundary expansion and density stratification. The abnormal microchannel vortex evolution and instability mechanisms/threshold are also discussed in detail in this article.