The AMS-02 experiment has reported a new measurement of the antiproton/proton ratio in Galactic cosmic rays (CRs). In the energy range $E\sim\,$60-450 GeV, this ratio is found to be remarkably constant. Using recent data on CR proton, helium, carbon, 10Be/9Be, and B/C ratio, we have performed a global Bayesian analysis based on a Markov-Chain Monte-Carlo sampling algorithm under a "two halo model" of CR propagation. In this model, CRs are allowed to experience a different type of diffusion when they propagate in the region close of the Galactic disk. We found that the vertical extent of this region is about 900 pc above and below the disk, and the corresponding diffusion coefficient scales with energy as $D\sim\,E^{0.15}$, describing well the observations on primary CR spectra, secondary/primary ratios and anisotropy. Under this model we have carried out improved calculations of antiparticle spectra arising from secondary CR production and their corresponding uncertainties. We made use of Monte-Carlo generators and accelerator data to assess the antiproton production cross-sections and their uncertainties. While the positron excess requires the contribution of additional unknown sources, we found that the new AMS-02 antiproton data are consistent, within the estimated uncertainties, with our calculations based on secondary production.