Highly conductive and transparent indium tin oxide (ITO) thin films, each with a thickness of 100 nm, were deposited on glass and Si(100) by direct current (DC) magnetron sputtering under an argon (Ar) atmosphere using an ITO target composed of 95% indium oxide and 5% tin oxide for photon-STM use. X-ray diffraction, STM observations, resistivity and transmission measurements were carried out to study the formation of the films at substrate temperatures between 40 and 400 ◦C and the effects of thermal annealing in air between 200 and 400 ◦C for between 1 and 5 h. The film properties were highly dependent on deposition conditions and on post-deposition film treatment. The films deposited under an Ar atmosphere pressure of 1.7×10−3 Torr by DC power sputtering (100W) at substrate temperatures between 40 and 400 ◦C exhibited resistivities in the range 3.0–5.7×10−5 Ωm and transmissions in the range 71%–79%. After deposition and annealing in air at 300◦C for 1 h, the films showed resistivities in the range 2.9–4.0×10−5 Ωm and transmissions in the range 78%–81%. Resistivity and transmission measurements showed that in order to improve conductive and transparent properties, 2 h annealing in air at 300 ◦C was necessary. X-ray diffraction data supported the experimental measurements of resistivity and transmission on the studies of annealing time. The surface roughness and film uniformity improve with increasing substrate temperature. STM observations found the ITO films deposited at a substrate temperature of 325 ◦C, and up to 400 ◦C, had domains with crystalline structures. After deposition and annealing in air at 300 ◦C for 1 h the films still exhibited similar domains. However, after deposition at substrate temperatures from 40 ◦C to 300 ◦C, and annealing in air at 300◦C for 1 h, the films were shown to be amorphous. More importantly, the STM studies found that the ITO film surfaces were most likely to break after deposition at a substrate temperature of 325 ◦C and annealing in air at 300◦C for 2 or 3 h. Such findings give some inspiration to us in interpreting the effects of annealing on the improvement of conductive and transparent properties and on the transition of phases. In addition, correlations between the conductive/transparent properties and the phase transition, the annealing time and the phase transition, and the conductive/transparent properties and the annealing time have been investigated.