A novel and reliable self-heating 2ω method has been developed to measure the Seebeck coefficient of the microscale/nanoscale thermoelectric materials. Based on the analytical solution of the transient heat-conduction equation of the specimen heated by a harmonic current, two measurement modes have been developed: (1) the Seebeck coefficient can be directly extracted from the ratio of experimentally measured 2ω Seebeck voltage to theoretically predicted 2ω temperature drop oscillation; and (2) the Seebeck coefficient can be steadily extracted from the measured 2ω and 3ω voltages. This approach has been applied to a 25.4 μm thick K-type thermocouple and the measured Seebeck coefficient corresponds well with the nominal value.