This article introduces a practical software architecture called CUBES, which focuses on system integration and evolvement for online virtual universities. The key of CUBES is a supporting platform that helps to integrate and evolve heterogeneous educational applications developed by different organizations. Both standardized educational applications that follow popular e-learning standards, such as SCORM and CELTS, and unstandardized ones can be integrated into CUBES with ease. A regularly used virtual university based on CUBES that includes educational applications covering the entire spectrum of the learning and management process is introduced to examine the usability of CUBES. The authors hope that new architectures, tools, and methods are explored to reduce the effort in building and evolving virtual universities.