For the design of virtual desktop, more natural, intuitive, and actual interaction styles have become the main design principle. In this paper, we present a virtual 3D desktop which integrates physics and bimanual input commands based on pen + touch. Objects on the desktop own physical properties, such as mass, dimensions, gravity etc. And they can be dragged casually and collide other objects under the effect of physical properties, just like we manipulate objects in the real word. We have designed a series of interaction techniques based on pen + touch input to support the desktop organization by observing people's operation behaviors in the real word. This novel interaction techniques making up the defects of input separately combines the advantages of touch input and pen input. A user survey experiment was designed to test the validity of the virtual desktop model. The result shows that the 3D desktop give the intuitive and actual feelings to users, and the interaction techniques we proposed is more efficient and natural.