To utilize magnetic skyrmions, nanoscale vortex-like magnetic structures, experimental elucidation of their dynamics against current application in various circumstances such as in confined structure and mixture of different magnetic phases is indispensable. Here, we investigate the current-induced dynamics of the coexistence state of magnetic skyrmions and helical magnetic structure in a thin plate of B20-type helimagnet FeGe in terms of in situ real-space observation using Lorentz transmission electron microscopy. Current pulses with various heights and widths were applied, and the change of the magnetic domain distribution was analyzed using a machine-learning technique. The observed average driving direction of the two-magnetic-state domain boundary is opposite to the applied electric current, indicating ferromagnetic s-d exchange coupling in the spin-transfer torque mechanism. The evaluated driving distance tends to increase with increasing the pulse duration time, current density (>1 × 109 A/m2), and sample temperature, providing valuable information about hitherto unknown current-induced dynamics of the skyrmion-lattice ensemble.