A thermoelectric nanowire array with a low heat leakage and a manufacturing method thereof are described. Nanowire array units separated from each other are formed on a substrate, and an air wall is formed at a region on the substrate free of the nanowire array units. Or, a polymeric material having a low thermal conductivity is combined with a template material so as to form a composite template structure for nanowires to deposit therein. With the design of the air wall or the composite template structure, the thermal reflow phenomenon of the thermoelectric nanowire array is avoided, thereby greatly improving a thermal dissipation efficiency of the thermoelectric nanowire array.