The present invention provides a waterproof cover structure with an array of microtubes, and the waterproof cover structure includes an elastic cover and an arrayed microtube unit watertight combined within a second opening of the elastic cover and having multiple microtubes formed in the arrayed microtube unit. Such waterproof cover structure with an array of microtubes not just covers an earphone and complies with the comfortable wearing requirements only, but also has the effects of providing a waterproof function by the formation of the arrayed microtube unit, balancing the pressure, temperature and humidity of internal and external auditory canals, and preventing sound distortion.
