Evolution of free-electron density in internal modification of glass by fs-laser pulses at high pulse repetition rates is simulated based on rate equation model, which is coupled with thermal conduction model in order to incorporate the effect of thermal ionization. Model shows that highly absorbing small plasma generated near the geometrical focus moves toward the laser source periodically to cover the region, which is much larger than focus volume. The simulated results agree qualitatively with dynamic motion of plasma produced in internal modification of borosilicate glass by fs-laser pulses at 1 MHz through the observation using high-speed video camera. The paper also reveals the physical mechanism of the internal modification of glass when heat accumulation is significant.