With the popularization of the new computation environment, internet, traditional software form has gradually not adapted the development and application under the internet environment. So a new generation software form with many characteristics such as independence, collaboration, response, evolution and multi-object, internetware is proposed. Its establishment depends on the effective collaboration among various distributed and asynchronous autonomous software entities in the opening environment. In the collaboration process, one important problem is how to effectively plan and adjust the topology structure among software entities to realize users’ demand in the dynamic environment. Aiming at this problem, several aspects including the organization and the assembling of the software entity and the evolvement of the topology are studied in this article, and concrete works include giving an internetware collaboration framework and flow model based on the Petri net and the mobile Agent technology, where the integrated model of internetware entities based on the Petri net reflects the ordered organization of the internetware entities in the problem space, and proving the support mechanism for the dynamically assembling among software entities based on the assembling model with the XML format, and using the influencing factors and the dynamic operation rules to describe several basic system evolvement activities.