The invention discloses a treatment method of carbonate-containing wastewater. The carbonate-containing wastewater passes through a regulating reservoir, a multi-medium filter, an ultrafiltration system, a reverse osmosis system, a primary resin softening system, a concentrated water reverse osmosis system, an advanced oxidation system, a tubular microfiltration system, a secondary resin softening system, a high-pressure reverse osmosis system, a sludge filter pressing system, an evaporation freezing crystallization system, an evaporation crystallization system, a wastewater treatment system, a recycling water tank and the like for process treatment to obtain sodium carbonate decahydrate product salt and by-products sodium sulfate and sodium chloride product salt. The treatment method has the advantages of strong anti-pollution capability, high concentration multiple, high recovery rate, high crystallized salt quality, high automation degree, low investment and low operation cost.