The reduction of setup time is very important in a lot production system. A punch press is a typical system of lot production. This paper describes a case study to reduce setup time of a punch press manufacturing system. Especially, this case study reduced the time of die exchange in the case that the standardization of die height is impossible realistically because of diversity on die height and heavy expenses. This study adopts a supplementary die and supplementary blocks to make the use of auto-clamping device possible. The paper also gives a sequencing algorithm to reduce the number of exchange of the supplementary die.