Boost factors of dark matter annihilation into antiprotons and electrons/positrons due to the clumpiness of dark matter distribution are studied in detail in this work, taking the Sommerfeld effect into account. It has been thought that the Sommerfeld effect, if exists, will be more remarkable in substructures because they are colder than the host halo, and may result in a larger boost factor. We give a full calculation of the boost factors based on the recent N-body simulations. Three typical cases of Sommerfeld effects, the non-resonant, moderately resonant and strongly resonant cases are considered. We find that for the non-resonant and moderately resonant cases the enhancement effects of substructures due to the Sommerfeld effect are very small ($sim mathcal{O}(1)$) because of the saturation behavior of the Sommerfeld effect. For the strongly resonant case the boost factor is typically smaller than $sim mathcal{O}(10)$. However, it is possible in some very extreme cases that DM distribution is adopted to give the maximal annihilation the boost factor can reach up to $sim 1000$. The variances of the boost factors due to different realizations of substructures distribution are also discussed in the work.
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