Sequence alignment is a fundamental problem in the computational biology. Many alignment methods have been proposed in the literature, such as pair-wise sequence alignment (2SA), syntenic alignment, multiple sequence alignment (MSA) and constraint multiple sequence alignment, etc. Three-sequence alignment (3SA) problem has been proposed and discussed in the computational biology and proved that the alignment results from 3SA are better than those from 2SA under some conditions. However, 3SA problem is less discussed over the past decade due to the computer capability. 3SA problem now is worthy to discuss due to the powerful computer and more and more genome and protein sequences. In this paper, an efficient parallel algorithm (P3SA) is proposed to solve 3SA problem. The P3SA method requires O(n2/p) space complexity and O(n3/p) time complexity. The experimental results show that P3SA algorithm is applicable and achieves a satisfied speed-up.