DNA data storage offers significant advantages, including high density and low energy consumption, making it a promising technology. However, the use of only four natural bases (A, T, C, G) limits the theoretical storage density to 2 bits/nt. Enzymatic methylation of DNA bases combined with nanopore sequencing provides an opportunity to exceed the theoretical density limits. However, homopolymers in DNA sequences can cause premature dissociation from Hel308 during sequencing, leading to reading failure. We propose the Methylation Base Huffman Compression Rotation Coding Strategy (MBHCRC), which incorporates methylation bases into the DNA storage system by transferring methyl groups to specific sites. This strategy uses a rotation coding method to prevent the formation of long homopolymers. Computer simulations of MBHCRC on various datasets, including documents, images, and audio files, demonstrate that storage density can reach 3.52 bits/nt for simple, highly repetitive data, and 1.52 bits/nt for general data. Both the maximum homopolymer length and GC content adhere to biochemical constraints. In conclusion, MBHCRC improves DNA storage density and addresses the issue of premature dissociation during nanopore sequencing, showcasing its potential for ultra high density and long-term data storage.