Theoretical studies have predicted that interactions between magnetic skyrmions and antiskyrmions give rise to various properties, such as unique arrangements, pair annihilation, topological transformation, and rectilinear and trochoidal motions that do not appear in only skyrmions or antiskyrmions. Recently, experimental studies have discovered that a Heusler material with the anisotropic Dzyaloshinskii–Moriya interaction shows a coexisting phase at 268 K and in-plane magnetic field-induced topological transformation of elliptical skyrmions and square-shaped antiskyrmions. Therefore, experimentally observing the coexisting phase and the topological transformation could be promising for developing skyrmion–antiskyrmion-based spintronics. However, such interactions and the detailed transformation mechanism remain unrevealed and unclear, respectively. Using Lorentz transmission electron microscopy experiments and micromagnetic simulations, we comprehensively study the properties in a coexisting phase of skyrmions and antiskyrmions in a Heusler material, Mn1.3Pt1.0Pd0.1Sn. Control of dipolar interaction (the sample thickness) allows us to realize a room-temperature coexisting phase. We find that the topological transformation occurs stochastically rather than deterministically, which can be explained by considering the magnetic point group and the direction of an in-plane magnetic field. We further observe isotropic long-range repulsive interaction between skyrmions and antiskyrmions in contrast to the conventional thought of the relative-position- and helicity-dependent short-range pairwise interactions, and deformation of skyrmions and antiskyrmions depending on the distance between them. Our simulations show that the deformation exerts significant influence on the magnetic energies and the energy landscape, contributing to the interaction. Our results provide insight into coexisting phases of skyrmions and antiskyrmions and a guide for developing skyrmion–antiskyrmion-based spintronics.