Bulk polythiophene material is usually regarded as thermal insulator because it has low thermal conductivity (less than 1 Wm-1K-1). However, the report demonstrates that along the amorphous polythiophene nanofiber axis, the pure polythiophene nanofibers have high thermal conductivity (more than 4.4 Wm-1K-1), which is obviously higher than that of the bulk polythiophene material. In order to throw light on this situation, molecular dynamics (MD) method is used to detect the high thermal conductivity of a polythiophene chain. However, the MD method is highly sensitive to the choice of empirical potential function or simulation method. Even if the same potential function (ReaxFF potential function) is adopted, the thermal conductivity of a polythiophene chain could also have obviously different results. To overcome the instability of MD method, we use the first-principles to calculate the force constant tensor. In such a case the properties of quantum mechanics in a polythiophene chain can be reflected. In our algorithm, several disadvantages of MD that different potential functions or different simulation methods probably lead to very different thermal conductivities for the same transport system are avoided. Based on the density functional theory (DFT), the central insertion scheme (CIS) method and nonequilibrium Green's function (NEGF) approach are used to evaluate the isotope effect on thermal transport in a polythiophene chain, which includes 448 atoms in a scattering region and has a length of 25.107 nm. It is found that the thermal conductivity of a 32-nm-long pure polythiophene chain reaches 30.2 Wm-1K-1, which is close to the thermal conductivity of lead at room temperature. The reduction of average thermal conductance caused by C atom impurity is more remarkable than by S for a pure polythiophene chain when the mixing ratios of 13C to 12C and 36S to 32S are equal. The most outstanding isotope effect on quantum thermal transport appears when the mixing ratio of 13C to 12C is 1:1. It will cause the average thermal conductance to decrease by at least 30% in the polythiophene chain at room temperature. Moreover, we find that the thermal conductance of a pure polythiophene chain is inversely proportional to the atomic weight of carbon, and increases nonlinearly with the increasing atomic weight of sulfur. It is of significance to optimize the thermal conductance properties of polythiophene function material.