With the exponential growth of the World Wide Web in recent years and the progress of information technology, the business market is changing its strategy for a modern online business environment. Autonomous Decentralized Database System(ADDS), based on autonomous coordinating subsystems, has been proposed as a system architecture in order to meet the innovative e-business requirements. Autonomy and decentralization of subsystems help achieving high response time in highly competitive situation and an autonomous Mobile Agent based coordination has been proposed to achieve flexibility in a highly dynamic environment. Further, this paper proposes the autonomous reconfiguration technology in ADDS in order to adapt the system to changing heterogeneous requirements. Based on the complementary requirements of the subsystems, heterogeneity distribution has been defined to accomplish the reconfiguration process. This autonomous reconfiguration technology consists of autonomous division and integration of the system, based on the ever-changing situation, to assure high response time. Simulation of the proposed technology shows its effectiveness for a large scale system and rapidly evolving situations.