To estimate the potential damage of buildings in various regions as soon as possible after an earthquake, this research employs the crowdsourcing technology to lever the smartphones in the buildings to estimate the fundamental natural frequency of the individual building to assist in disaster relief. This study uses the accelerometer embedded in the smartphones to measure acceleration response of the buildings during earthquake excitations, and uses Wi-Fi Direct technology to synchronize the acceleration data. After uploading it to the server and aligning the acceleration direction, the system identification method is used to obtain the fundamental natural frequency of the buildings. Two system identification methods are the output-only ones and the input-output ones. The output-only system identification methods including the Frequency Domain Decomposition (FDD) and Stochastic Subspace Identification (SSI) methods and the input-output ones including the Combined stochastic and deterministic Subspace Identification (CSI) and Frequency Response Function (FRF) methods are employed in this study. In case the ground motion is not available, only the output-only system identification methods can be used in system identification methods. However, according to the results of numerical simulations, even under ideal situation, i.e., time is synchronized, orientation aligned, and without noise, the estimated fundamental natural frequency using the output-only system identification methods is not reliable because they are affected by the characteristic of earthquake excitations. Therefore, an algorithm to identify the ground motion signals from the measured time history of different smartphones is proposed. Based on the assumption that the ground motion signals are available, the input-output system identification methods can be used. The results of numerical simulation indicate that whether time synchronization has a great influence on the CSI approach and whether orientation alignment has a great influence on the FRF approach. Shaking table tests of a four-story steel building were conducted to verify the proposed methods. The results show that the maximum frequency error and root-mean-square-error using CSI with time synchronization and without orientation alignment are 0.9% and 0.5% respectively, while the ones using FRF with time asynchronization and orientation alignment are 3.5% and 1.1% respectively. This trend is similar to the numerical simulation. Therefore, it is suggested to use CSI when time synchronization is valid, and use FRF instead when time synchronization is not available.