Provided is a method of manufacturing a sensor structure, where vertically-well-aligned nanotubes are formed and the sensor structure having an excellent performance can be manufactured at the room temperature at low cost by using the nanotubes. The method of manufacturing a sensor structure includes: (a) forming a lower electrode on a substrate; (b) forming an organic template having a pore structure on the lower electrode; (c) forming a metal oxide thin film in the organic template; (d) forming a metal oxide nanotube structure, in which nanotubes are vertically aligned and upper portions thereof are connected to each other, by removing the organic template through a dry etching method; and (e) forming an upper electrode on the upper portions of the nanotubes.