Through the sequential-recirculation and cross-recirculation ways, the two-stage micro-aerobic EGSB reactor system was operated to treat the actual coking wastewater. And the removal efficiencies of SCN−-N, CN−-N, NH3-N, NO3 −-N and TN in coking wastewater were investigated, and then the mechanism of simultaneous and efficient removal of NH3-N, NO3 −-N and TN in coking wastewater was also analyzed. The results showed that, using the two-stage micro-aerobic EGSB reactor to treating actual coking wastewater, for the sequential recirculation way and the cross-recirculation way, the removal efficiencies of SCN−-N, CN−-N, NH3-N, NO3 −-N, TN were 98.0%, 91.5%, 81.3%, 30.4%, 24.5% and 97.3%, 97.0%, 92.7%, 92.0%, 70.9%, respectively. And the two-stage micro-aerobic EGSB reactor system could achieve simultaneous and efficient removal of ammonia and TN in the coking wastewater through the cross-recirculation way. For the sequential recirculation two-stage micro-aerobic EGSB reactor system, high SCN−-N and NO3 −-N removal of 94.2% and 90.8% was accomplished in the EGSBI, and high NH3-N removal of 89.8% could attain in the EGSBII. However, high NO3 −-N accumulation in the EGSBII also caused very low TN removal of 24.5% for the two-stage micro-aerobic EGSB reactor system. High SCN−-N removal in the EGSBI could ensure high NH3-N removal in the EGSBII. More importantly, the EGSBI had a very strong ability to support SCN−-N shock. For the cross-recirculation two-stage micro-aerobic EGSB reactor system, the EGSBI could keep simultaneous and efficient removal of SCN−-N, CN−-N, NH3-N, NO3 −-N and TN (93.5%, 92.4%, 84.1%, 92.0% and 73.7%). When using sequential recirculation way, thiocyanate-degrading bacteria could form competitive inhibition to ammonia oxidizing bacteria in the EGSBI, and thus, simultaneous and efficient removal of SCN−-N and NH3-N could not accomplish in the EGSBI. High concentration NO3 −-N in the EGSBI was removed mainly through denitrification. However, through the cross-recirculation way for the two-stage micro-aerobic EGSB reactor system, the effluent recirculation of the EGSBI and/or the EGSBII were changed from simple high NH3-N to mixed recirculation of high NH3-N+high NO3 −-N and/or from high NO3 −-N to high NH3-N+high NO3 −-N, respectively. Consequently, thiocyanate-degrading bacteria, denitrifying bacteria and anammox bacteria could keep high activity at the same time and also the effective coupling of denitrification and anammox bacteria was realized in the EGSBI and EGSBII, and which ensured the simultaneous and efficient removal of SCN−-N, NH3-N and NO3 −-N in the EGSBI and EGSBII, and finally realized the simultaneous and efficient removal of NH3-N, NO3 −-N and TN in the two-stage micro-aerobic EGSB reactor system.