With the continuous increase in the number of irregular buildings, ensuring the safety of building structures has become the primary concern. The study used finite element analysis to estimate the natural frequency of vibration of irregular building structures, and further designed a fuzzy control algorithm combined with magnetorheological dampers to improve their seismic performance. The research results showed that the longitudinal and transverse natural frequencies of Model 1 were 10.44 Hz and 10.51 Hz, respectively, while those of Model 2 were 10.31 Hz and 9.89 Hz, respectively. Using the fuzzy control method, the peak displacement of the building structure was reduced to 11.64 cm, and the peak acceleration was 7.9 m/s2. Comparing the open-plus-closed-loop control with open-loop control methods, it was found that although the fluctuation amplitude of the open-loop control method was relatively large, its control effect was poor, while the open-plus-closed-loop control methods had good overall control effect, with the peak acceleration of 8.26 m/s2 in the open-loop control. The study provides an accurate method for estimating the natural vibration frequency of irregular building structures and demonstrates the effectiveness of the designed fuzzy control algorithm in controlling building vibration.