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We examine the space-time structure of particle-emitting source and two-pion interferometry in a smoothed hydrodynamic model with fluctuating initial conditions. An equation of state with a crossover tran-sition between quark-gluon plasma and hadronic gas is adopted in the description of the system evolution. We find that the fluctuating initial conditions lead to inhomogeneons particle-emitting sources. The interferometry results of R_s and Ro indicate that both the source size and the duration of pion emission decrease when the freeze-out temperature increases. The values of R_o/R_s obtained by our simulated two-pion interferometry are consistent with the previous results of smoothed particle hydrodynamics, and smaller than those calculated in usual hydrodynamic models.