A channel layout of a flat-plate micro pulsating heat pipe (MPHP) for an excessively localized heating condition is proposed. The excessively localized heating condition is implemented using a small heater, which covers only about 2% of the whole area, in the middle of the bottom part. To simplify the heat transfer characteristics in MPHPs, the channel regions are modeled as a region with the high effective thermal conductivity, and the topology optimization method is employed to determine a distribution of the channel regions of the MPHP. The constraints on the maximum length scale and the minimum solid volume fraction in local regions are imposed to take into account the operational characteristics of MPHPs. In the proposed channel layout, which is inspired by the topology optimization result, the channels are laid out in such a way that some channels are merged to reduce the number of channels. Due to a decrease in the number of channels, all channels are able to overlap the localized heating section without any thermally-isolated channel. To verify the effectiveness of the proposed method, the MPHPs with the channel layout designed by topology optimization and two kinds of channel layouts for the references are fabricated, and their flow characteristics and thermal performances are experimentally compared. In case of the MPHP with the uniform channel layout, only 4 channels out of 18 channels overlap the heating section, and the stagnant liquid slugs in the thermally-isolated channels are observed. On the other hand, in the MPHP with the channel layout designed by topology optimization, all channels overlap the heating section, and the active oscillating motion of the liquid slugs occurs in all channels. This allows the MPHP with the channel layout designed by topology optimization to have about two times higher thermal performance than the MPHP with the uniform channel layout. In this study, the channel layout of the MPHP for the excessively localized heating condition is firstly suggested, and the experimental results show that the proposed channel layout can effectively overcome the limitation associated with the localized heating condition.