Pulping wastewater still contains massive refractory organics after biotreatment, with high colority, low biodegradability, and lasting biotoxicity. To eliminate refractory organics in pulping wastewater, a methanotrophic co-metabolic system in a gas cycle Sequencing Batch Biofilm Reactor (gcSBBR) seeded by soil at a ventilation opening of coal mine was quickly built on the 92nd day. The removal rate of COD, colority and TOC was 53.28%, 50.59% and 51.60%, respectively. Analysis of 3D-EEM indicated that glycolated protein-like, melanoidin-like or lignocellulose-like, and humic acid-like decreased by 7.85%, 5.02% and 1.74%, respectively. Moreover, this system exhibited high activity of soluble methane monooxygenase (sMMO) and mmoX encoding sMMO reached up to 7.89 x 10(5) copies/mu L. Methanotrophs, namely, Methylocaldum (8.28%), Methylococcus (6.06%) and Methylomonas (0.07%), were detected by 16S rRNA sequencing. And other bacteria were dominated by Denitratisoma, Anaerolineaceae_uncultured and Methylophilaceae_uncultured. Refractory organics was biodegraded through the synergy among microorganisms, and a postulated synergy pathway was put forward.