We present the measurement of the diffractive structure function of the antiproton in proton-antiproton collisions at the center-of-mass energy of 1.8 TeV. The data were collected during the 1995-1996 Tevatron collider run using the Collider Detector at Fermilab~(CDF). Diffractive events are characterized by the recoil $\bar{p}$ and the forward rapidity gap in the fnal state. In order to tag the recoil $\bar{p}$, we installed a Roman-pot type antiproton spectrometer~(RPS), and using the forward calorimeter and the beam-beam counter, we identify the rapidity gap. In order to identify a hard collision, we require the presence of two or more jets. In this analysis, we calculate the hard scale in the interaction~($Q^2$), the momentum fraction of antiproton carried by struck parton~($\xpb$), and the fractional momentum of the struck parton in the exchanged object~($\beta$). We obtained the diffractive structure function as a function of $\beta$ and $Q^2$ in the kinematic region of $0.035\leq\xi\leq 0.095$ and $|t|\leq 1$ GeV${}^2$. We observe no $Q^2$ dependence in the diffractive structure function of the antiproton in the $Q^2$ region measured in this study. This is consistent with the H1 result at HERA $ep$ collider experiment. The absolute value of the diffractive structure function measured at CDF is smaller than that of the H1 result by, approximately, a factor of 1/7. The discrepancy is also observed in other results at CDF such as the diffractive W and b-quark production where the cross section is about 20\% of the prediction using the Donnachie-Landshoff pomeron flux. These results suggest that the diffractive cross section is not described by using the universal diffractive structure function of the antiproton.