We propose a new variational method for treating short-range repulsion of bare nuclear force for nuclei in antisymmetrized molecular dynamics (AMD). In AMD, the short-range correlation is described in terms of large imaginary centroids of Gaussian wave packets of nucleon pairs in opposite signs, causing high-momentum components in nucleon pair. We superpose these AMD basis states and name this method high-momentum AMD (HM-AMD), which is capable of describing strong tensor correlation (Prog. Theor. Exp. Phys. (2017) 111D01). In this paper, we extend HM-AMD by including up to two kinds of nucleon pairs in each AMD basis state utilizing the cluster expansion, which produces many-body correlations involving high-momentum components. We investigate how much HM-AMD describes the short-range correlation by showing the results for $^3$H using the Argonne V4$^prime$ central potential. It is found that HM-AMD reproduces the results of few-body calculations and also the tensor-optimized AMD. This means that HM-AMD is a powerful approach to describe the short-range correlation in nuclei. In HM-AMD, momentum directions of nucleon pairs isotropically contribute to the short-range correlation, which is different from the tensor correlation.