Thermoelectric performance of Ca3Co4O9 system has been enhanced through the misplaced substitution with Cr doping at Ca‐sites. The study of Cr doping at Co‐sites has also been performed for comparing. Base on the analysis of the structural data, we conclude that the doped Cr ions should be in the form of Cr+6, and enter into Ca‐sites of Ca2CoO3 layers in Ca3−xCrxCo4O9 lattice and Co‐sites of CoO2 layers in Ca3Co3.90Cr0.10O9 lattice, respectively. As Cr ions are doped into Ca‐sites in Ca3−xCrxCo4O9 lattice, both resistivity and thermopower increase obviously, while thermal conductivity decreases. Among all samples, Ca2.95Cr0.05Co4O9 shows the maximum ZT value, which is enhanced by 12% than that of Ca3Co4O9. The results show that the misplaced substitution with a proper Cr doping at Ca‐sites is beneficial to the enhancement of the thermoelectric performance in Ca3Co4O9 system compared to the traditional idea: Cr doping at Co‐sites, which is suggested to originate from the combined action of the carrier concentration, the electronic correlation, and the lattice disharmony.