Recently, a self-propagating high-temperature synthesis (SHS) technique has been discovered for the low-cost and ultra-fast preparation of Cu2SnSe3. In this research, the reaction mechanism of the ultra-fast SHS process during the synthesis of Cu2SnSe3 was investigated in detail, and the thermoelectric properties of the compacted bulk by PAS (Plasma Activated Sintering) were discussed. Nearly single phased Cu2SnSe3 could be prepared by the SHS reaction in 1.5 s, and a high combustion wave speed of 6.7 mm/s was found in this process. The quenching experiment and the multi-step experiments verified that, the SHS synthesis of Cu2SnSe3 from raw elements was majorly composed of three individual SHS processes from Cu-Se, Sn-Se and CuSe-SnSe, in which the speed of combustion wave was estimated to be 5 mm/s, 18 mm/s and 3 mm/s, respectively. The SHS-PAS prepared Cu2SnSe3 possessed superior electrical properties and thermal properties as compared to samples prepared by other methods, and thus possessed a relatively higher thermoelectric figure of merit ZT across the entire measuring temperature range. The Cu2SnSe3 prepared by SHS-PAS acquired the highest ZT of 0.53 at 750 K. A very low lattice thermal conductivity of 0.61 Wm−1K−1 at 750 K was achieved in the SHS-PAS synthesized Cu2SnSe3, which was due to the structure distortion caused by different cations and the strengthened phonon scattering introduced by in-situ formed nano-precipitates. The discovery of the SHS reaction mechanism would be instructive for the reliable and mass production of Cu2SnSe3.