Molecular weight (MW) is an important factor affecting compost DOMs chemical properties and environmental behavior. However, the current understanding of the MW distribution of compost DOM still needs to be clarified. This study employed ultrafiltration to separate the different MW fractions from the DOM in mushroom residue compost (MRC) and rice straw compost (RSC). Subsequently, different compost-derived MV fractions distributions and spectral characteristics were comprehensively investigated. The results of the dissolved organic carbon (DOC) revealed that HMW DOM (>10 kDa) was the major fraction in MRC and RSC, accounting for 80% and 71% of DOC, respectively. Meanwhile, MMW DOM (5~10 kDa) and LMW DOM (<5 kDa) represented 12%~15% and 9%~15% of the total DOC, respectively. These findings suggested that HMW DOM would play a crucial role in determining DOMs chemical composition and molecular structure in compost. Moreover, the results of spectral characteristic parameters, such as SUVA254, E2/E3 and HIX, indicated that the degree of aromatization and humification of MW DOM showed a similar trend in the order of HMW>MMW>LMW. In contrast, the BIX and FI values showed an opposite distribution. These findings evidenced that HMW DOM enriched in unsaturated conjugated structures, such as aromatic rings, while MMW and LMW DOM contained high autogenetic contributions. The three-dimensional fluorescence-parallel factor analysis demonstrated that the compost DOM and its MW fractions were primarily composed of three types of humus (C1—C3) and one protein (C4). HMW DOM in MRC and RSC consisted mainly of long-wavelength humic acid (C3), which accounted for 34% and 85% of the total fluorescence intensity of HMW fractions in MRC and RSC DOM, respectively. MMW and LMW DOM were mostly composed of fulvic acid (C1, 41%~53%) and short-wavelength humic acid (C2, 25%~36%). The infrared spectroscopy (FTIR) analysis showed that the HMW DOM contained more hydrophobic benzene ring structures. In contrast, MMW and LMW fractions contained more hydrophilic oxygen-containing functional groups, such as carbonyl and carboxyl groups. Overall, our findings advanced the understanding of the chemical composition and molecular structure of compost DOM and provided crucial data for further evaluation of the maturation, stabilization, and environmental behavior of compost.