Recent years have seen a rapid development of machine learning based multi-module unmanned aerial vehicle (UAV) systems. To address the oracle problem in autonomous systems, numerous studies have been conducted to use metamorphic testing to automatically generate test scenes for various modules, e.g., those in self-driving cars. However, as most of the studies are based on unit testing, also known as end-to-end model-based testing, a similar testing approach may not be equally effective for UAV systems where multiple modules are working closely together. Therefore, in this paper, instead of unit testing, we propose a novel metamorphic system testing framework for UAV, named MSTU, to detect the defects in multi-module UAV systems. A preliminary evaluation plan to apply MSTU on an emerging autonomous multi-module UAV system is also presented to demonstrate the feasibility of the proposed testing framework.