Molybdenum oxide (MoO3) electrochromic (EC) materials have not been widely used at present due to relatively poor performance and inadequate research. In order to enhance the EC properties of the MoO3 to achieve the purpose of practical use, the modified nanocrystalline MoO3 films were fabricated by a cheap and simple complexation-assisted sol–gel method followed by annealing at 300 °C. In this method, dopamine (DA) is used as a structure-directing agent and the added amount of DA has a great influence on the structure and morphology and, thus, electrochemical and EC properties of the MoO3 films. Different from the pure MoO3 polycrystalline film, the film modified with a suitable amount of DA possesses a distinctive nanocrystal-embedded amorphous structure, and, thus, can achieve synergy effects of EC properties through combining the advantages of both amorphous phases and nanocrystalline. Therefore, compared with the pure MoO3 film, the modified MoO3 film shows much higher EC properties in terms of optical contrast, coloration efficiency, switching speed, and cycling stability. Moreover, a complementary type EC device with dual active layers (the modified MoO3 film and polyaniline) was fabricated and tested, and the results demonstrate the potential application of the modified MoO3 film.