The development of p-channel tin oxide thin-film-transistors spurred the research into microstructural analysis of tin oxide phases and control of conduction type, as it is widely known that tin oxide thin films exhibit both n- and p-type conduction depending on growth conditions. This study reports the relationship between the microstructural properties and the ambiguity of the electrical conduction type observed in nonstoichiometric tin oxides. Nonstoichiometric tin oxide thin films have been produced by RF magnetron sputtering with a dependence on the growth gas atmosphere. The crystal phase of the tin oxide deposited under low ambient oxygen content was mainly SnO1+x with relatively stable p-type conduction. On the other hand, for deposition under high ambient oxygen content, phase separation with structural modulation in the tin oxide film occurred in SnO-like and SnO2-like regions. These phases with different conduction types caused electrically unstable dual conduction types in the tin oxide films, despite their low electrical resistivity.