A detailed interpretation of the detected emission lines of environments where propyne (or methyl acetylene, CH$_3$CCH) is observed requires access to its collisional rate coefficients with the most abundant species in the interstellar medium, namely, helium (He) or molecular hydrogen (H$_2$). We present the first three-dimensional potential energy surface (3D PES) for the CH$_3$CCH-He molecular complex. We study the dynamics of the collision and report the first set of rate coefficients for temperatures up to 100 K for the collisional excitation of the lowest 60 ortho rotational levels and 60 para rotational levels of CH$_3$CCH by He atoms. We computed the 3D PES with the explicitly correlated coupled-cluster with a single-, double-, and perturbative triple-excitation method in conjunction with the augmented correlation-consistent triple zeta basis set (CCSD(T)-F12a/aug-cc-pVTZ). The 3D PES was then fitted to an analytical function and scattering computations of pure rotational (de-)excitation of CH$_3$CCH by
collision with He atoms were performed. State-to-state cross-sections were computed using the close coupling method for
total energies up to 100 cm$^ $ and with the coupled states approximation at higher energies for both the ortho- and para- symmetries of CH$_3$CCH. The PES we obtained is characterised by a large anisotropy and a potential well depth of 51.04 cm$^ $. By thermally averaging the collisional cross-sections, we determined the quenching rate coefficients for kinetic temperatures up to 100 K. A strong and even $ j$ propensity rule at almost all collision energies is present for CH$_3$CCH-He complex. To evaluate the impact of rate coefficients on the analysis of observations, we carried out non-local thermodynamic equilibrium (non-LTE) radiative transfer computations of the excitation temperatures and we demonstrate that local thermodynamic equilibrium (LTE ) conditions are not typically fulfilled for the propyne molecule.