We applied the flexible and logic-reconfigurable VME boards to many control systems, which requires fast and real-time control, such as a tag generating system and a pulse motor controller of 60Hz beam shutter. The board has a field programmable gate arrays (FPGA) chip for execution of user logic, which can be implemented in C. IO interfaces of the board are module cards. They can be mounted on the base board with connectors. The board was easily　modified by exchanging the IO modules and reconfiguring FPGA logic. We also upgraded the base board. The new board supports large data transition. The new board has PMC sockets with a PCI bus and a Gigabit Ether port. The same IO module card can also be used on the new board. and the upgraded board are shown in the presentation. The design and implementation of developing-evironment of the user logic of the board are shown with the applications. We also discuss about the design of the upgraded board.