The instability of the Marangoni toroidal flows in microchannels is of interest in various areas such as microfluidics and heat transfer. Using pure liquid as working fluid in this study, the phenomena of Marangoni symmetry-to-asymmetry transition which does not arise from the buoyancy was observed. The experiments used a vertical cylindrical channel and the meniscus was formed at the bottom outlet to minimize the buoyant influences. Two microscopes were used to have top view and side view of the meniscus simultaneously. The Marangoni flow field on the meniscus was obtained by means of tracing particles. It was observed that the Marangoni flow on a concave meniscus was always nearly symmetrical, while that on a convex meniscus was out of symmetry with only one single vortex occupying the whole channel. The experimental results were highly consistent to the simulation results of authors' previous 3D numerical model (Pan and Wang in Microfluid Nanofluid 9:657, 2010). Theoretical analysis together with newly developed numerical models is employed to dig into the mechanisms. The inward (from the meniscus edge to the center) Marangoni flow is found not as stable as the outward one. Based on the heat transfer analysis, a concave meniscus always has a colder edge thus the flow is outward and stable; while a convex enough meniscus could have an inward flow thus not stable and tends to lose the symmetry. The amplification mechanism of the inward Marangoni flow is comprehensively explained. Two conditions are required for the inward flow to lose the symmetry, i.e., the bulk liquid must be warmer than the meniscus, and the Marangoni number must be above a certain small value.