Guide Positioning Sequencing (GPS) is a novel method for genome-wide DNA methylation detection. The generated sequencing data has the advantages of low detection cost and no sequence preference. At present, the most important step in methylation analysis is to align the sequences to the reference genome. However, the existing method uses Smith-Waterman for local sequence alignment, which takes too much time and affects the mapping efficiency. Therefore, a new alignment algorithm for the GPS data is proposed. The algorithm uses the advantages of paired-end sequencing to determine the alignment positions. The methylation sequences are first aligned to the reference genome, and then corresponding regular sequences are used to determine the final positions. The experimental results show that compared with the existing method, the method presented in this paper has a high mapping efficiency with comparable accuracy and the time performance improved by more than 3 times.