Flexible and accurate control of microswimmers is significant for lots of applications. Herein, we present a method for effective microswimmer manipulation in multiple microfluidic systems by thermal buoyancy-capillary convection. In the microdevice, four strips of microheaters arranged at the bottom of the microchannel are used to unevenly heat microfluids, and the convection flow forms under the influence of gravity and interfacial tension gradient. By adjusting the DC signals applied on these four heating elements, the intensity and direction of convection flow can be flexibly adjusted. Accordingly, granular samples dispersed in liquid buffer can be controllably driven to the target position by the Stokes drag. The swimming behavior of polystyrene (PS) microspheres at the solid-liquid interface of the device is first investigated. It shows that the PS microswimmers can migrate along various geometrical patterns by powering the microheaters with designed voltage combinations, and the migration velocity is positively affected by the increased voltage. Then, the butyl acrylate (BA) microswimmers are manipulated at the gas-liquid interface of the microchip. It turns out that the BA microswimmers migrate oppositely compared with PS swimmers under the same energization strategy. Additionally, the translation direction of BA swimmers can be changed over a 360° range by different voltage combinations. The multifunctionality of our approach is further demonstrated by conveniently driving the trimethylolpropane triacrylate microswimmers at the liquid-liquid interface of the microplatform along different directions and pathlines. Therefore, this technique can be promising for many cases needing granular sample control, such as cargo delivery and sensing.