<p>Haplotypes of polyploid organisms provide important insights into polyploid evolution and advanced breeding strategies. Significant challenges remain in polyploid haplotype phasing, including the great number of haplotype copies and the presence of haplotypes with high local sequence similarity. We present nTChap, a new reference-based polyploid phasing algorithm for long reads, which applies an iterative procedure involving a two-round clustering and consensus construction to generate accurate haplotypes. Using simulated datasets, we show that nTChap outperforms current tools in terms of accuracy and error rates, while maintaining robust performance across high-ploidy genomes and low-coverage data. We then show that nTChap assembles reasonable haplotype structures using real datasets.</p>