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DNA methylation is essential for the survival of bacteriophages (phages), yet, we know little about the methylation of their genomes. Here, we analyze the methylomes of 9,665 metagenome-assembled high-quality human gut phages using single-molecule real-time sequencing. We show that gut phages universally use DNA methylations to escape from host defense systems, and reveal factors that correlate with methylation densities, including coding potential, gene function, and phage lifestyle. Strikingly, more than a third of the phages encode their own DNA methyltransferases (MTases). These phages have increased genome methylation densities, and are more abundant and prevalent than those without MTases. Most MTases are closely homologous to gut bacterial ones, and have been likely exchanged during phage-bacterial host interactions. As gut phages can share ~15% of their genes with gut bacteria at 90% protein similarity, a fast evolving, complex phage-bacterium interaction network can be assumed that shapes both phage and host fitness.