Seismic behavior of a structure is directly related to its dynamic characteristics, which include natural frequency, damping ratio, and mode shape. This study focuses on the long-term monitoring of dynamic characteristics of six selected target structures. The covariance-driven stochastic subspace identification (SSI) approach is used to estimate the fundamental natural frequency and damping ratio of target buildings based on long-term motion records in order to examine the temporal variation of dynamic properties. The fundamental natural frequency and damping ratio variations over time are first discussed. It is found that the fundamental natural frequency of some structures reduces dramatically after the 2011 Tohoku Earthquake, accompanied by a rise in damping ratio. Then, regression analysis is used to assess the relationship between dynamic characteristics and ground motion parameters (Peak ground acceleration (PGA), magnitude, focal depth, and epicentral distance) and structural response (root mean square acceleration, maximum response amplitude). It is discovered that the identified natural frequency has no clear correlation with the focal depth, a slight negative correlation with the epicentral distance, and a strong negative correlation with the magnitude and PGA. The root mean square acceleration and the maximum response amplitude are negatively correlated to the target buildings’ natural frequencies. Finally, the influence of environmental factors on dynamic properties is investigated.