The invention discloses a parallel universal sequence alignment method running on a multi-core computer platform. The parallel universal sequence alignment method comprises the following steps: firstly performing classification on to-be-aligned sequence sets by utilizing a clustering method (Cluster) to obtain subsequence sets (C1, C2, ... , Cm) unequal in size; then, distributing to-be-aligned subsequence sets to all computing cores (Core1, Core2, ... , Coren) by applying a distribution method (Distribute), wherein load balance on each core is taken as the final goal of distribution; subsequently, respectively aligning (Align) all the subsequence sets by applying the traditional sequence alignment method; finally, merging aligned subsequence sets by applying a merging method (Merge) to obtain final alignment results of the to-be-aligned subsequence sets. According to the parallel universal sequence alignment method disclosed by the invention, upon the multi-core computer platform, by fully utilizing data parallel computing strategy, the processing efficiency of biological sequence alignment is obviously improved.