In this study, we reported the effects of the boron (B) substitution into the Ca site in the Ca3Co4O9 system on the electrical, thermal and magnetic properties between 300 K and 5 K. The results indicated that the B-substitution into the system caused an increase of resistivity due to the decrease on carrier concentration. Thermal conductivity decreased for the x = 0.5 B-substituted sample and then increased with increasing the B-content. Analysis on the thermal conductivity of samples showed that the phonon–phonon interaction term is the dominant component in the total thermal conductivity for all the samples. It was found that the point defect contribution to the thermal conductivity increased by increasing the B-content. The temperature dependence of magnetic susceptibility showed a paramagnetic behavior at room temperature and ferrimagnetic behavior below 20 K for unsubstituted sample. But, the magnetization decreased in the B-substituted samples. The substitution of B into the Ca site destroyed the interlayer coupling, which resulted in the decrease of the ferromagnetic behavior. The susceptibility data was fitted using Curie–Weiss law with temperature independent term and the μeff values were calculated to be 1.42 μB and 3.89 μB for unsubstituted sample and the highest B-substitution, respectively.