Thermoelectric properties of the Ca 3 Co 4 O 9 system have been enhanced through an exotic route: Na doping at Co site, namely misplaced substitution. To compare, we have also performed the research of Na doping at Ca site and Co vacancy. In view of the analysis of XRD, XPS, and Raman data, Na + ions could be suggested to enter into Co sites of [CoO 2 ] layers in Ca 3 Co 4−x Na x O 9 (x = 0, 0.05, 0.10) and Ca sites of [Ca 2 CoO 3 ] layers in Ca 2.90 Na 0.10 Co 4 O 9 , respectively. And Co ions are omitted from [CoO 2 ] layers in Ca 3 Co 3.90 O 9 . Among all samples, Ca 3 Co 3.90 Na 0.10 O 9 shows the maximum ZT value, which at room temperature reaches to ∼0.0117. Such a value is about 150% larger than that of Ca 3 Co 4 O 9 and 63% larger than that of Ca 2.90 Na 0.10 Co 4 O 9 . The results indicate that the misplaced substitution is more beneficial to enhance the thermoelectric performance of Ca 3 Co 4 O 9 system, compared with the traditional idea with Na doping at Ca site. Such an enhancement is mainly attributed to the combined action of electronic correlation, locally modified band structure near Fermi level, and carrier concentration.