A manufacturing method of asymmetric bumps is provided. First, a substrate is provided. A film layer is then formed on the substrate. Next, a complex photomask including at least one transparent region, a number of opaque regions, and a number of semi-transparent regions is provided. Each of the semi-transparent regions is disposed between two adjacent opaque regions, and at least one light-shielding pattern is randomly disposed in each of the semi-transparent regions. The film layer is then patterned with use of the complex photomask, and multiple asymmetric bumps are formed on the substrate. By using the complex photomask, manufacturing steps of the asymmetric bumps can be reduced. Besides, a manufacturing method of a pixel structure having the above-mentioned asymmetric bumps is also provided.