A novel method based on online cleanup mode combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was established. After an automated sample cleanup system with aqueous gel column, sulfonamides in chicken were detected in multiple reaction monitoring (MRM) mode. The total run time of the system, which included automated extraction, analytical chromatography and re-equilibration, was within 30 min. Different experimental processes containing extraction, purification, separation, and detection have been evaluated respectively to obtain optimized parameters. The developed method was fully validated and the efficient and superior performance of the developed method was demonstrated. The method produced linear results for all sulfonamides from 1 to 10 ng g−1 with a linearity >0.99. The intra-day precision of the method was <8.45% while the inter-day precision was <9.11%. The matrix effect was 77.5% to 105.1%. The recovery was in the range of 72.66% to 116.7% for all sulfonamides. The limit of quantitation in the chicken was 0.6 ng g−1 and the limit of detection was 0.2 ng g−1. Compared with traditional procedures, the automated sample clean-up strategy could significantly shorten the analysis time and offer higher detectability, with the advantage of sufficient sensitivity. Also, the use of gel chromatography column employed the water phase and reduced the organic reagent to achieve the level of green chemistry.