The invention relates to a method and system for quickly arranging multiple windows and mobile apparatus thereof. A method and a system for quickly arranging multiple windows and a mobile apparatus are provided. The method for the mobile apparatus with a touch screen includes monitoring a window arrangement driving event at an application layer and when the window arrangement driving event is generated, transferring the window arrangement driving event from the application layer to a frameworks layer. The method also includes identifying a current arrangement mode and selecting a new arrangement mode according to the current arrangement mode; obtaining the window objects currently operated on the mobile apparatus; calculating a display position and a display size for each of the obtained window objects according to the new arrangement mode; and displaying the window objects on the touch screen of mobile apparatus according to the calculated display position and display size. Accordingly, the window objects can be quickly arranged by the method to effectively enhance the efficiency of multi-operation on the mobile apparatus.