We study the formation of non-linear structures in Warm Dark Matter (WDM) models and in a Long-Lived Charged Massive Particle (CHAMP) model. CHAMPs with a decay lifetime of about 1 yr induce characteristic suppression in the matter power spectrum at subgalactic scales through acoustic oscillations in the thermal background. We explore structure formation in such a model. We also study three WDM models, where the dark matter particles are produced through the following mechanisms: i) WDM particles are produced in the thermal background and then kinematically decoupled; ii) WDM particles are fermions produced by the decay of thermal heavy bosons; and iii) WDM particles are produced by the decay of non-relativistic heavy particles. We show that the linear matter power spectra for the three models are all characterised by the comoving Jeans scale at the matter-radiation equality. Furthermore, we can also describe the linear matter power spectrum for the Long-Lived CHAMP model in terms of a suitably defined characteristic cut-off scale k Ch , similarly to the WDM models. We perform large cosmological N -body simulations to study the non-linear growth of structures in these four models. We compare the halo mass functions, the subhalo mass functions, and the radial distributions of subhalos in simulated Milky Way-size halos. For the characteristic cut-off scale k cut = 51 h Mpc −1 , the subhalo abundance -2 -(∼ 10 9 M sun ) is suppressed by a factor of ∼ 10 compared with the standard ΛCDM model. We then study the models with k cut ≃ 51, 410, 820 h Mpc −1 , and confirm that the halo and the subhalo abundances and the radial distributions of subhalos are indeed similar between the different WDM models and the Long-Lived CHAMP model. The result suggests that the cut-off scale k cut not only characterises the linear power spectra but also can be used to predict the non-linear clustering properties. The radial distribution of subhalos in Milky Way-size halos is consistent with the observed distribution for k cut ∼ 50 − 800 h Mpc −1 ; such models resolve the so-called "missing satellite problem".