The progress of new technologies makes virtual reality (VR) easier, and inexpensive head-mounted displays (HMDs) accelerate the development of advanced VR services. The advantage of the technologies is to offer the better immersion of a VR world, to use natural user interface (NUI) devices and to operate them with a user’s gesture. The problem to use NUI devices for VR-based services is to take into account various types of NUI devices. We need to consider how a user to use NUI devices in a proper way, in particular, when an HMD limits his/her view of the real world. Our approach to solve the problem is to use an affordance that offers implicit information how to navigate VR-based services. However, there are a little researches to investigate the relationship between different types of NUI devices and the design of proper affordances to navigate VR-based services. The paper provides some insights how respective types of NUI devices influence affordance design to navigate VR-based services. For extracting effective insights, we have developed two VR-based services, where we discuss two types of operating methods and three types of affordances for respective operating methods are examined. Also, we chose two types of NUI devices for navigating the VR-based services. Then, we conducted some experiments to extract some insights as a guideline to develop future VR-based services. The result shows that the differences among respective NUI devices may not significantly influence affordance design, however have strong effects on understanding how to navigate VR-based services. The understanding also affects how each user prefers which NUI devices, because NUI devices require us to use gesture to navigate the services, but the intuition that differs in each individual is important.