This paper implements dual-kernel system using standard Linux and real-time embedded Linux for the real-time control of intelligent robot systems. Such system provides more useful services including standard Linux thread that is easy to implement complicated tasks and real-time tasks for the deterministic response to velocity control. Here, an open source real-time embedded Linux, XENOMAI, is ported on embedded target board. And for interfacing with motor controller we adopted a real-time serial device driver. The real-time task was implemented with a priority to keep the cyclic control command for trajectory control. In order to validate deterministic response of the proposed system, the performance measurement of the delay in performing trajectory control with feedback loop is evaluated with non real-time standard Linux. The proposed software architecture is anticipated to take advantage of features in both standard Linux and real-time operating systems for the intelligent robot systems.