As one of the three essential components of ground motions, the duration of ground motions significantly influences the seismic response and damage state of buildings. To investigate the influence of long-duration ground motions on the seismic response of masonry structures, the authors selected 40 pairs of well-matched long and short duration ground motions from literature as input and used a numerical model of an equivalent frame of a typical masonry structure as the analytical object to analyze the influence of long-duration ground motions on the fragility of masonry structures. The results showed that long-duration ground motions will result in a higher probability of structural failure compared to short-duration ground motions, and the increase Δf in the probability of failure caused by long-duration ground motions on the masonry structure is dependent on the seismic intensity Sa(T0) and limit states, in three specified limit states it increases with increasing Sa(T0) initially, reaches a peak value, and then decreases with further increase in Sa(T0); In the first limit state (boundary between none or slight damage and moderate damage), Δf can reach up to 50.0%. In the second limit state (boundary between moderate damage and heavy damage), Δf can reach up to 53.1%. In the third limit state (boundary between severe damage and collapse), Δf reach up to 45.1%.