The cosmic antideuteron is a promising probe for the dark matter annihilation signature. In order to determine the DM signature, the background astrophysical antideuteron flux should be carefully studied. In this work we provide a new calculation of the secondary antideuteron flux, and pay special attention to the uncertainties from hadronic interaction models by using several Monte Carlo generators. The uncertainties from propagation effects are also carefully investigated for both the astrophysical background and DM annihilation signature in several scenarios, which are constrained by the latest B/C ratio measured by AMS-02. Considering these uncertainties, we find that the secondary antideuteron flux is hard to detect in the near future detectors. However, the antideuteron signature from dark matter annihilation will be detectable even considering the constraint from the AMS-02 observation of the $bar{p}/p$ ratio.
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