Abstract: As an effective probability tool, seismic collapse fragility has been widely used in structural seismic collapse capacity assessment. Traditional collapse fragility analysis typically considers only a single earthquake action and only the uncertainty associated with the ground motion records. However, strong mainshocks are often followed by aftershocks, and significant uncertainty also exists in structural design parameters. When structures are in the state of imminent collapse, they exhibit highly nonlinear behavior. And, the coupled effect of structural uncertainty and aftershocks can detrimentally impact the structural collapse capacity. To address this issue, this study conducted a seismic collapse fragility analysis considering aftershock and structural uncertainty. Two reinforced concrete frames designed according to Chinese codes were selected as the case-study structures. Ten structural parameters related to loading condition and material properties were considered as the uncertainty parameters. Mainshock-aftershock sequences were constructed using the repeated, randomized, and decaying methods. A stochastic mainshock-aftershock incremental dynamic analysis (IDA) method was proposed by integrating Correlation reduction-based Latin Hypercube Sampling (CLHS) into the mainshock-aftershock IDA. The method was employed to analyze the mainshock-aftershock collapse capacity of the case-study structures, generating mainshock-aftershock collapse fragility curves. Comparative analyses revealed that the aftershocks reduced the structural collapse capacity, and the coupled effect of structural uncertainty and aftershocks leaded to a further reduction in collapse capacity by up to 20%. Moreover, the structural uncertainty increased the dispersion of the mainshock-aftershock collapse fragility, and also increased the collapse probability by up to 60%.