Fluorine-doped tin oxide (FTO) thin films were deposited on glass substrates using ultrasonic spray pyrolysis (USP) at a fixed substrate temperature of 400 ◦C and various Fluorine/Tin (F/Sn) atomic ratios of 0, 0.1, 0.5, and 1.0. Effects of F/Sn atomic ratios on structural-morphological, compositional, electrical, optical, and nanomechanical properties of the FTO thin films were systematically studied. The FTO films exhibited a tetragonal structure with preferred orientations of (110), (200), and (211), and polycrystalline morphology with spear-like or coconut shell-like particles on the surfaces. The presence of F-doping was confirmed by XPS results with clear F1s peaks, and F-concentration was determined to be 0.7% for F/Sn = 0.1 and 5.1% for F/Sn = 0.5. Moreover, the resistivity of FTO films reduced remarkably from 4.1 m Ωcm at F/Sn = 0 to 0.7 m Ωcm at F/Sn = 1, primarily due to the corresponding increase of carrier concentration from 2 × 1020 cm−3 to 1.2 × 1021 cm−3. The average optical transmittance of the films prepared at F/Sn of 0–0.5 was over 90%, and it decreased to 84.4% for the film prepared at F/Sn = 1. The hardness ( H) and Young’s modulus ( E) of the FTO films increased when the F/Sn ratios increased from 0 to 0.5, reaching maximum values of H = 12.3 ± 0.4 GPa, E = 131.7 ± 8.0 GPa at F/Sn = 0.5. Meanwhile, the H and E reduced considerably when the F/Sn ratio further increased to 1.0, following the inverse Hall-Petch effect approximately, suggesting that the grain boundary effect played a primary role in manipulating the nanomechanical properties of the FTO films. Furthermore, favorable mechanical properties with large H/Ef and H3 /E2f ratios were found for the FTO film prepared at F/Sn = 0.5, which possessed high crystallinity, large grain size, and compact morphology.