The invention discloses a shallow trench structure cleaning method, an isolation structure manufacturing method, and a semiconductor device. A shallow trench structure comprises a substrate, a shallow trench located in the substrate, and a dielectric mask layer located on the substrate. The cleaning method comprises the following steps: carrying out the first cleaning of the shallow trench structure, so as to remove residuals in the shallow trench; and carrying out the second cleaning of the shallow trench structure through employing phosphoric acid solution after the first cleaning. In the method, the phosphoric acid solution can corrode the above reaction products and peels off the reaction products, thereby reducing the reaction products generated in a cleaning process of the shallow trench structure. Meanwhile, the phosphoric acid solution can achieve the back etching of the dielectric mask layer, thereby increasing the exposure area of the top of the shallow trench, and enabling the top of the shallow trench to be easier to round at step of forming linear oxide on an inner wall of the shallow trench.