Real-time monitoring on displacement and acceleration of a structure provides vital information for people in different applications such as active control and damage warning systems. Recent developments of the Internet of Things (IoT) and client-side web technologies enable a wireless microcontroller board with sensors to process structural-related data in real-time and to interact with servers so that end-users can view the final processed results of the servers through a browser in a computer or a mobile phone. Unlike traditional structural health monitoring (SHM) systems that deliver warnings based on peak acceleration of earthquake, we built a real-time SHM system that converts raw sensor results into movements and rotations on the monitored structure’s three-dimensional (3D) model. This unique approach displays the overall structural dynamic movements directly from measured displacement data, rather than using force analysis, such as finite element analysis, to predict the displacement statically. As an application to our research outcomes, patterns of movements related to its structure type can be collected for further cross-validating the results derived from the traditional stress-strain analysis. In this work, we overcome several challenges that exist in displaying the 3D effects in real-time. From our proposed algorithm that converts the global displacements into element’s local movements, our system can calculate each element’s (e.g., column’s, beam’s, and floor’s) rotation and displacement at its local coordinate while the sensor’s monitoring result only provides displacements at the global coordinate. While we consider minimizing the overall sensor usage costs and displaying the essential 3D movements at the same time, a sensor deployment method is suggested. To achieve the need of processing the enormous amount of sensor data in real-time, we designed a novel structure for saving sensor data, where relationships among multiple sensor devices and sensor’s spatial and unique identifier can be presented. Moreover, we built a sensor device that can send the monitoring data via wireless network to the local server or cloud so that the SHM web can integrate what we develop altogether to show the real-time 3D movements. In this paper, a 3D model is created according to a two-story structure to demonstrate the SHM system functionality and validate our proposed algorithm.