A design of integrated controller（IC） with high-performance embedded systems for hydroelectric generating unit is proposed. IC should be replaced existing programmable logic controller（PLC）， which can not meet the requirement of electromagnetic compatibility standards and lacks enough functions. The design of IC not only improves the unit controller's standard， but also solves problems when use PLC such as: inflexible communication protocol， not suitable for dedicated I/O modules， complicated system design. It makes hydroelectric generating unit controller have the flexibility to access various intelligent equipment， protection devices and special automatic devices， which implements share of data collection. IC can flexibly extend dedicated I/O modules to implement specific functions which can not be completed by PLC such as: AC acquisition， flexible configuration of the sequence record of events， temperature cyclic detection， unit automatic synchronization， human-computer interaction， recollection of failure etc. It optimizes the entire hydroelectric generating units so that now the system has advantages of simplified design， easy to maintain， investment savings and so on.