Fertilization is one of the essential managements to maintain and increase soil organic carbon (SOC) level in agroecosystems. It has been realized that fertilizer applications influenced the turnover of labile and refractory organic carbon pools in arable soil markedly. However, the dynamic of relatively refractory lignin in response to fertilization is still kept unclear. Therefore, the impact of long-term organic fertilization on the content and degradation degree of lignin in Mollisol was investigated. Lignin monomers were released by alkaline CuO oxidation method and quantified by gas chromatography (GC). At the time scale of decades, lignin was clearly accumulated in soil and the relative accumulation of lignin in SOC was evident after long-term organic fertilizer application. Compared with the unfertilized soil, lower acid to aldehyde ratios of vanillyl and syringyl units induced by organic fertilization suggested a lower degradation degree of lignin incorporated into soil to some extent. It could be concluded that long-term organic fertilization was an effective fertilizer practice for lignin accumulation in soil and SOC sequestration in Mollisol in northeast of China.