The ultra-high accuracy indoor and outdoor localization is fundamental for a variety of applications such as industrial automation, Internet of Things and structure monitoring. However, many approaches based on optical methods, ultrasound and computer vision may suffer from insufficient coverage, obstruction or high computing load. In traditional GNSS and radar-like microwave system, further efforts are needed to enhance the accuracy and availability. Now we demonstrate a microwave localization system with ultra-stable frequency synchronization net based on an inverse GNSS scheme. Such a combination effectively improves both the coverage and accuracy since the frequency synchronization net in free space can cover kilometer-level area and serves as reference for phase difference process. The stability of frequency synchronization net is better then $10^{-13}$/s. The ranging resolution is 25 micrometers and the Mean Squared Error (MSE) of three-dimensional localization is 16 micrometers.