The invention provides an MBR wastewater treatment system with deep denitrification and dephosphorization functions. The MBR wastewater treatment system sequentially comprises an anaerobic pool, a front anoxic pool, an aerobic pool, a rear anoxic pool and a membrane pool. The membrane pool does not contain an aeration part, a membrane set device realizes reciprocating motion through a mechanical transmission device, thus the membrane pollution problem is effectively solved, MBR process aeration energy consumption is further reduced, and the situation that the content of water outlet total nitrogen is increased due to excessive oxidation of sludge is further avoided. Through improvement for the membrane pool, the membrane pool directly returns a flow to the anaerobic pool, a process flow return form is simplified, and meanwhile, the situation that the biological dephosphorization effect is affected by flow return of DO and excessive nitrate nitrogen is further avoided. Through partitionaeration, the content of the DO of the control tail end of the aerobic pool is less than 0.1 mg/L, and the denitrification effect of the rear anoxic pool is improved, a flow return point and a rear dosing point are arranged at a middle section in the rear anoxic pool, thus denitrification of an internal source and an external source can be realized simultaneously, the denitrification cost is reduced, and when a carbon source is added externally, it can be ensured that the content of the water outlet total nitrogen is less than 1 mg/L. The MBR wastewater treatment system is used for municipalwastewater treatment and can realize earth surface IV-type water outlet when the carbon source is not added externally, wherein the content of TN is less than 5 mg/L, and the content of TP is less than 0.2 mg/L.