For the first time, details of the spatial and temporal acceptable evolution of the merging process of co-rotating electron vortices in a potential well are successfully captured using a “single-shot method” with a high temporal resolution of 10 µs. Four-electron filaments are trapped inside the Beam eXperiment-Upgrade linear trap [H. Himura, Nucl. Instrum. Methods Phys. Res. A 811, 100 (2016)] with a uniform axial magnetic field and co-axial multi-ring electrodes. Images of non-emitting electron filaments are captured using a high-speed camera with up to 1 000 000 fps, a microchannel plate, a fast-decay phosphor screen of which fluorescence duration is 0.15 µs, and a super fine metallic mesh with an open area ratio of 89%. Images captured every 10 µs clearly show the growth of multiple short-wave instabilities in the wing trailing electron vortices. The experimental methods and measurement techniques presented in this paper can contribute to revealing exactly how small vortices evolve into a large structure or turbulence in a potential well through complex processes.