The use of Linux in the domain of embedded systems is growing very fast. Due to the complexity of hardware and software on Linux-based platforms, it is challenging to meet the performance requirements, especially for the mixed-criticality system with both real-time and best-effort tasks. We propose a reference design of Linux-based mixed-criticality system using PREEMPT_RT patch to improve real-time performance and QEMU/KVM virtual machine to reduce interferences. An evaluation environment of the proposed design is built with recent software and hardware to investigate the performance characteristics via experimental measurements. We measure and analyze the baseline kernel latency, the system throughput and the real-time performance under multiple conditions. In detailed analysis, we reveal novel insights on the real-time capabilities and limitations of Linux-based embedded systems. The results show that our design can meet the 100µs deadline goal of 1kHz real-time task with high probability under various extreme interferences, and can deliver high throughput for best-effort workload.