The 2008 Iwate-Miyagi Nairiku earthquake ($M_w$ 6.9, $M_{jma}$ 7.2) occurred on 14 June 2008 in Japan. The amplification and asymmetric waveform of the vertical acceleration at the ground surface recorded by accelerometers at station IWTH25, situated 3 km from the source, were remarkable in two ways. First, the vertical acceleration was extremely large (PGA = 38.66 $m/s^2$ for the vertical component, PGA = 42.78 $m/s^2$ for the sum of the three components). Second, an unusual asymmetric waveform, which is too far above the zero acceleration axis, as well as large upward spikes were observed. Using a multidegree-of-freedom (MDF) system consisting of a one-dimensional continuum subjected to vertical acceleration recorded at a depth of 260 m below ground level, the present paper clarifies numerically that these singular phenomena in the surface vertical acceleration records occurred as a result of the jumping and collision of a layer in vertical motion. We herein propose a new mechanism for such jumping and collision of ground layers. The unexpected extensive landslides that occurred in the area around the epicenter are believed to have been produced by such jumping under the influence of vertical acceleration.