The invention belongs to the technical field of treatment of desulfurization wastewater and particularly provides a membrane separation combination zero-emission system for deeply treating desulfurization wastewater with a whole membrane method. The system comprises a pretreatment water tank, a water quality regulating water tank, a first reaction tank, a sedimentation water tank, a second reaction tank, a concentrated water tank, an TMF (tubular micro-filtration) assembly, a produced water tank and an NF (nanofiltration) assembly which are sequentially communicated through a pipeline, wherein a produced water outlet of the NF assembly is connected and communicated with an SWRO (seawater reverse osmosis) assembly through a pipeline, a concentrated water outlet of the SWRO assembly is connected and communicated with a DTRO (disk tubular reverse osmosis) assembly through a pipeline, and a concentrated water outlet of the NF assembly is communicated with a wastewater collecting tank through a pipeline. With the adoption of the membrane separation combination zero-emission system for deeply treating desulfurization wastewater with the whole membrane method, the pure water recovery rate is higher, the occupied area is small, the cost is low, resource utilization is realized, membrane assemblies cannot be blocked by dirt, stable operation of the membrane system is guaranteed, the wastewater treatment efficiency is improved, resource waste is avoided, and meanwhile, unnecessary environmental pollution is reduced.