Understanding the correlation mechanism of side chains on thermal transport of organic semiconductors is crucial for functionalized organic electronics. In this study, phenyl and alkyl side chains, two representatives of side chain engineering, are chosen to modify dinaphtho-[2,3-b:2',3'-f]thieno[3,2-b]thiophene (DNTT) to synthesize Ph-DNTT and C10-DNTT. The thermal conductivities of the three organic semiconductors exhibit obvious anisotropy, and the corresponding relationships are along-chain > inter-chain > cross-chain. The phenyl side chains enhance the thermal conductivity in the along-chain direction and degrade it in the inter-chain direction, while the alkyl side chains hinder thermal transport. In the cross-chain direction, side chains have a slight effect on thermal transport. The structure orientation consistency between the phenyl side chains and the main chains in Ph-DNTT leads to phonon coupling in the along-chain direction, which improves phonon transport. In the inter-chain direction, the combined effect of the phonon group velocity and phonon participation ratio causes the thermal conductivity degeneracy of Ph-DNTT. For C10-DNTT, the vibrational mismatch between the alkyl side chains and the main chains results in the degradation of thermal transport in the along-chain and inter-chain directions. In the cross-chain direction, the nonbonding interaction dominates the energy transfer in the three organic semiconductors, which induces inferior phonon transport properties and weak effects of side chains.