Molecular clouds have a hierarchical structure from few tens of parsecs for giants to few tenth of a parsec for proto-stellar cores. Nowadays, our observational techniques are so advanced that it has become possible to detect the small-scale substructures inside the molecular cores. The question that arises is how these small condensations are formed. In the present research, we study the effect of ambipolar diffusion heating on the ubiquitous perturbations in a molecular cloud and investigate the possibility of converting them to dense substructures. For this purpose, a small azimuthal perturbation is implemented on the density of an axisymmetric two-dimensional cylindrical cloud, and its evolution is simulated bythe technique of two-fluid smoothed particle hydrodynamics. Theself-gravity is not included and the initial state has uniformdensity, temperature and magnetic field, parallel to theaxis of cylinder. In addition, all perturbed quantities are assumed todepend onlyon azimuth angle and time. Computer experiments show that if theambipolar diffusion heating is ignored, the perturbation willbe dispersed over the time. Including the heating due to ambipolardiffusion heats the matter in regions adjacent to the perturbation, thus,leading to the transfer of matter into the perturbed area. In this case, the density of perturbations can be increased. Also, the results ofsimulations show that an increase of the initial magnetic pressureleads to the intensification of difference between density ofperturbations and their surroundings (i.e. increasing of density contrast). This effect is due to the direct relationship of the drift velocity to the intensity of the magnetic field and its gradient. Simulations with different initial uniform densities show that the growth of relative density contrast is more clear with a special density. This result can be explained by the intensification of thermal instability in this special density.