Disclosed is a waterproof earphone structure including a main body with a rear cavity and a front cavity for installing a waterproof module and a shielding module respectively, and a speaker body installed in the main body. The waterproof module includes first and second waterproof elements installed in the rear and front cavities of the main body respectively. This structure not just allows users to sense external sounds only, but also improves low-frequency noise interference and water-resistance. Since the first and second waterproof elements are formed with pores having a diameter smaller than 0.6 mm and arranged apart from one another, external low-frequency noises are suppressed. Further, the effect of surface tension prevents water from entering into waterproof devices or soaking the interior of the earphone. Users enjoy good sound quality since the sound is transmitted through the pores. In addition, the shielding module provides an anti-dust effect.