Boreal wetlands are significant natural sources of methane (CH4) to the atmosphere, and are vulnerable to freezing-thawing cycles (FTC). Nonetheless, the underlying factors that induce CH4 emission in boreal wetlands during FTC are still unclear. Our goal was to characterize soil CH4 emission potential from a freshwater marsh as impacted by FTC and to determine the corresponding mechanisms. We collected soil samples from two soil layers (0–20 and 20–40 cm) of an undisturbed freshwater marsh in Sanjiang Plain, Northeast China, and subjected them to various freezing (6 to −6 °C) and thawing (−6 to 6 °C) cycles. Soil CH4 emission, DOC, and the aromaticity and complexity of DOC indexes were monitored. The results showed that FTC significantly increased CH4 emission potential in the 0–20 cm surface soil layer. The maximum hourly CH4 emission rate was 55.0 mg C m−2 h−1, approximately 19 times as high as that of the unfrozen control sample (2.8 mg C m−2 h−1). However, the peak intensity of CH4 emission decreased when the numbers of FTC increased. Meanwhile, FTC not only increased the quantity of DOC released, but also enhanced its instability via increasing the contribution of relatively small, readily degradable organic molecules. Additionally, the CH4 emission potential was significantly correlated with the aromaticity and complexity of DOC, indicating that the release of labile substrates under FTC was one important factor controlling the microbial production of CH4 and the high emissions upon thawing. Our study suggested that global warming-induced increases in seasonal FTC in boreal wetlands may increase CH4 emissions beyond what would occur from long-term temperature increases alone.