Abstract: Positioning navigation and timing (PNT) is the nation's critical infrastructure. At present, China has established the relatively complete ground-based augmentation systems, satellite-based augmentation systems and low earth orbit(LEO) satellite-based augmentation system for comprehensive PNT. Although indoor positioning on a contemporary smartphone is booming, including Wi-Fi, bluetooth, magnetic field fingerprinting, and so on, these existing methods still cannot provide high quality PNT services for the whole area, such as underground, indoor space, and underwater. Recently, the key technologies of real three-dimensional model and digital twin model received more and more attention. The information of geographic scene presents unrecalled opportunities to improve the robust availability, continuity, high accuracy and reliability of comprehensive PNT system. First, we introduce the state-of-the-art of related studies of scene-based augmentation systems, including scene-based PNT systems augmentation.Second, we summarize the challenges and present the definition and basic concept of the scene-based augmentation systems for comprehensive PNT. Next, the system architecture, construction units and hierarchical service mechanism of scene-based augmentation systems is proposed. Finally, we forecast the development trend of scene-based augmentation systems for comprehensive PNT. The China comprehensive PNT system should be BeiDou-centered and include ground-based augmentation systems, satellite-based augmentation systems (SBAS), LEO SBAS and scene-based augmentation systems for comprehensive PNT as auxiliary augmentation systems. It has the ability to provide intelligent PNT services in whole area.