The carrier transport mechanism in most thermoelectric semiconductors is governed by conventional band transport, however, there is an exception in ternary Cu2SnSe4 (CTS) or its based counterparts in which the transport mechanism is dominated by a small polaron hoping model. The sluggish movement of the small polaron greatly suppresses the mobility of the carrier due to the strong coupling of the electron with the phonon, therefore, a proper decoupling is highly necessary. To achieve this goal, herein, InSe bonds are created by incorporating some indium into the cation vacancy in CTS, which effectively balances the transports between electron and phonon. As a consequence, both the electrical property (σ) and thermal conductivity (κ) are optimized in the sample Cu2Sn1−xInxSe4 (x = 0.1), and its thermoelectric performance improves with the highest figure of merit (ZT) of 0.5. This value is ≈52% higher than that of the pristine CTS, proving that incorporation of In in the cation vacancy in CTS is an alternative way to balance the transports between electron and phonon.