Serials of Mn doping by substituting Cd sites on Cu2CdSnSe4 are prepared by the melting method and the spark plasma sintering (SPS) technique to form Cu2Cd1-xMnxSnSe4. Our experimental and theoretical studies show that the moderate Mn doping by substituting Cd sites is an effective method to improve the thermoelectric performance of Cu2CdSnSe4. The electrical resistivity is decreased by about a factor of 4 at 723 K after replacing Cd with Mn, but the seebeck coefficient decreases only slightly from 356 to 289 μV/K, resulting in the significant increase of the power factor. Although the thermal conductivity increases with the doping content of Mn, the figure of merit (ZT) is still increased from 0.06 (x = 0) to 0.16 (x = 0.10) at 723 K, by a factor of 2.6. To explore the mechanisms behind the experimental results, we have performed an ab initio study on the Mn doping effect and find that the Fermi level of Cu2CdSnSe4 is shifted downward to the valence band, thus improving the hole concentration and enhancing the electrical conductivity at the low level doping content. Optimizing the synthesis process and scaling Cu2Cd1-xMnxSnSe4 to nanoparticles may further improve the ZT value significantly by improving the electrical conductivity and enhancing the phonon scattering to decrease the thermal conductivity.