Control Cyber-Physical Systems (CPSs) constitute a major category of CPS. In control CPSs, in addition to the well-studied noises within the physical subsystem, we are interested in evaluating the impact of cross-domain noise: the noise that comes from the physical subsystem, propagates through the cyber subsystem, and goes back to the physical subsystem. Impact of cross-domain noise is hard to evaluate when the cyber subsystem is a black box, which cannot be explicitly modeled. To address this challenge, this article focuses on the two-level control CPS, a widely adopted control CPS architecture, and proposes an emulation based evaluation methodology framework. The framework uses hybrid model reachability to quantify the cross-domain noise impact, and exploits Lyapunov stability theories to reduce the evaluation benchmark size. We validated the effectiveness and efficiency of our proposed framework on a representative control CPS testbed. Particularly, 24.1% of evaluation effort is saved using the proposed benchmark shrinking technology.