Disclosed are a microaspiration-based lung window apparatus for obtaining a microscopic image of in vivo lung tissue and a method for using the window apparatus to obtain cell-level and molecular level microscopic images of in vivo lung tissue while maintaining physiological respiration and circulation of an animal without interference. In one embodiment, a lung window apparatus comprises an open window having the upper and lower parts open, a cover glass placed over the upper part and lung tissue coming in contact with the lower part; an aspiration tube extending from one side of the open window to an aspiration apparatus enabling the inside of the open window to be in a vacuum state; and a tilting mount placing unit extending from one side of the open window having a tilting mount to enable the cover glass and an object lens of a confocal microscope system to stay parallel to each other.