The manufacturing systems have to cope with the circumstance that the requirements of customers are changed abruptly and the life cycle of product becomes short. In this paper, to develop the efficient control and operation of autonomous, distributed machining systems the concept of Holonic Manufacturing System is adopted and methods for the control and operation of the system are proposed including an evaluation function for the negotiation between holons. And it is applied to scheduling and selection of operations to be worked with consideration of quality. It is expected that the proposed methods may be applied to operate autonomous, distributed machining systems.