Dissolved organic matter (DOM) is involved in numerous biogeochemical processes, and its molecular weight affects many of these processes through its bioavailability and sorptive capacity. However, it remains unknown to what extent the molecular weight of DOM mediates its dynamics, for example, influencing its role in DOM-microbe interactions and the processes determining the compositional assembly of DOM. To address this issue, ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and high-throughput sequencing were applied to investigate how the molecular weight of DOM was associated with its dynamics in two typical agricultural soils with different fertility. Our results showed that low-molecular-weight DOM had lower biological stability and a higher transformation potential. Analysis of the DOM-microbe co-occurrence network showed that low-molecular-weight DOM displayed tighter interactions with a diversity of microbes, while high-molecular-weight DOM interacted with only a few microbes. Ecological null models revealed that the compositional assembly of low-molecular-weight DOM, but not high-molecular-weight DOM, was more controlled by deterministic processes. Taken together, our results demonstrate the fundamental role the molecular weight of DOM plays in determining biological stability, transformation potential, interactions with microbes, and assembly mechanisms of DOM in agricultural soils. This work provides the foundation for general principles explaining complex dynamics of DOM in natural ecosystems, highlighting that using theories and concepts in metacommunity ecology, such as community diversity and assembly mechanisms, may open a new avenue to understand DOM dynamics from a macro perspective.