Accurately quantifying biological age is crucial for understanding the mechanisms of aging and developing effective interventions. Molecular aging clocks, particularly epigenetic clocks that use DNA methylation data to estimate biological age, have become essential tools in this area of research. However, the lack of a comprehensive, publicly accessible database with uniformly formatted DNA methylation datasets across various ages and tissues complicates the investigation of epigenetic clocks. Researchers face significant challenges in locating relevant datasets, accessing key information from raw data, and managing inconsistent data formats and metadata annotations. Additionally, there is a lack of dedicated resources for aging-related differentially methylated sites (DMSs, also named differentially methylated positions or differentially methylated cytosines) and regions (DMRs), which hinders progress in understanding the epigenetic mechanisms of aging. To address these challenges, we developed MethAgingDB, a comprehensive DNA methylation database for aging biology. MethAgingDB includes 93 datasets, with 11474 profiles from 13 distinct human tissues and 1361 profiles from 9 distinct mouse tissues. The database provides preprocessed DNA methylation data in a consistent matrix format, along with tissue-specific DMSs and DMRs, gene-centric aging insights, and an extensive collection of epigenetic clocks. Together, MethAgingDB is expected to streamline aging-related epigenetic research and support the development of robust, biologically informed aging biomarkers.