We examine an effect of acoustic phonon scattering on an electric conductivity of single-component molecular conductor [Pd(dddt)$_2$] (dddt = 5,6-dihydro-1,4-dithiin-2,3-dithiolate) with a half-filled band by applying the previous calculation in a two-dimensional model with Dirac cone [Phys. Rev. B {bf 98},161205 (2018)], where the electric transport by the impurity scattering exhibits the noticeable interplay of the Dirac cone and the phonon scattering,resulting in a maximum of the conductivity with increasing temperature. The conductor shows a nodal line semimetal where the band crossing of HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital) provides a loop of Dirac points located close to the Fermi energy followed by the density of states (DOS) similar to that of two-dimensional Dirac cone. Using a tight-binding (TB) model [arXiv:2008.09277], which was obtained using the crystal structure observed from a recent X ray diffraction experiment under pressure, it is shown that the obtained conductivity explains reasonably the anomalous behavior in [Pd(dddt)$_2$] exhibiting almost temperature independent resistivity at finite temperatures. This paper demonstrates a crucial role of the acoustic phonon scattering at finite temperatures in the electric conductivity of Dirac electrons. The present theoretical results of conductivity are compared with those of experiments.