The combine harvester is considered as an important but complicated and costly machine. The appropriate size of combine has to be developed to use efficiently in Korea. But the combine is such a complicated machine that a complete design model to develop a new type is impossible without understanding the relationship between each factor. The combine capacity is generally limited by the cleaning shoe performance. So a design model for a cleaning shoe has to be developed first for the complete combine design. The objective of this research was to develop a cleaning model of head-feeding combine to predict grain separation from chaff and broken straw on a sieve. A developed physically based model can explain the situation which can happen during separation process. A test apparatus based on the field going machine was developed. The test materials were paddy rice and barley. The data obtained were analyzed by the hand and the video camera. The developed model was verified as an adequate model through the test with $R^2$ of 0.934 and 0.837. The model can be used to evaluate design and operation alternatives of combine and also applied to the automatic control of separation unit of combine with a loss monitering sensors.