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Underwater glider, being a new kind of underwater autonomous robot which has no external propulsion system equipped on it, is driven depending on buoyancy adjustment of itself. In development of underwater glider, its control system design plays an important role. The paper put forward the design approach to build embedded control system based on a real-time kernel in underwater glider. Hardware configuration of the control system is designed, in which SysCentreModuleTM-7108B main-board and M-System DOC2000 flash memory serve as core. The methods that drive DiskOnChip under QNX as well as QNX kernel migration to M-System DOC2000 are given. Main content and fundamental frame of system boot file - BuildFile which suitable for the embedded control system is created. Control system software modules applied in underwater glide is described and some of them were developed. All application software is supported by QNX real-time kernel and ultimately resided on DOC together with QNX. Theoretical analysis and some simulation experiments prove that the design idea is correct and the implementation approach is feasible.