The DSMC modeling is developed to simulate three-dimensional (3D) rarefied ionization flows and numerically forecast the communication blackout around spacecraft during hypervelocity reentry. A new weighting factor scheme for rare species is introduced, whose key point is to modify the corresponding chemical reaction coefficients involving electrons, meanwhile reproduce the rare species in resultants and preserve/delete common species in reactants according to the weighting factors. The resulting DSMC method is highly efficient in simulating weakly inhomogeneous flows including the Couette shear flow and controlling statistical fluctuation with high resolution. The accurate reliability of the present DSMC modeling is also validated by the comparison with a series of experimental measurements of the Shenzhou reentry capsule tested in a low-density wind tunnel from the HAI of CARDC. The obtained electron number density distribution for the RAM-C II vehicle agrees well with the flight experiment data, while the electron density contours for the Stardust hypervelocity reentry match the reference data completely. In addition, the present 3D DSMC algorithm can capture distribution of the electron, N + and O + number densities better than the axis-symmetric DSMC model. The introduction of rare species weighting factor scheme can significantly improve the smoothness of the number density contours of rare species, especially for that of electron in weak ionization case, while it has negligible effect on the macroscopic flow parameters. The ionization characteristics of the Chinese lunar capsule reentry process are numerically analyzed and forecasted in the rarefied transitional flow regime at the flying altitudes between 80 and 97 km, and the simulations predict communication blackout altitudes which are in good agreement with the actual reentry flight data. For the spacecraft reentry with hypervelocity larger than the second cosmic speed, it is forecasted and verified by the present DSMC modeling that ionization reactions will cover the windward capsule surface, leading to reentry communication blackout, and the communication interruption must be considered in the communication design during reentry in rarefied flow regimes.