High dense Bi2Te3 nanowire arrays were fabricated in porous anodic alumina (PAA) by electrochemical deposition. A macro-integration measurement was used to study the thermoelectric properties of a superimposed layer of Bi2Te3/PAA structure. In this macro-integration system, meaningful amounts of heat will transport along Bi2Te3 nanowire arrays, and so the measurement errors of micro-current and micro-temperature difference of individual nanowire can be eliminated. The influences of wire diameter, area fraction of wires and interface thermal resistance in the sandwich structure on the measurement accuracy of Seebeck coefficient and electrical conductivity of Bi2Te3/Al2O3 system were discussed. The experimental electrical conductivity is close to the theoretically calculated value. Further improvement in eliminating the interface thermal resistance would bring more reliable result in Seebeck coefficient measurement. The macro-integration measurement is a practical method to evaluate the thermoelectric properties of thermoelectric nanowire arrays.