The invention provides a cleaning agent for removing emulsion deposits and a preparation method and application of the cleaning agent. The cleaning agent for removing the emulsion deposits comprises,by 100 parts of weight, 10-30 parts of glycol ether compounds and esterification products of glycol ether compounds and alkyl carboxylic acid compounds, 10-40 parts of a double alkyl chain quaternaryammonium salt cationic surfactant, 0.1-5 parts of polyether amine compounds, 0-10 parts of a corrosion inhibitor, 0-10 parts of a defoaming agent and the balance water or saline water. The invention further provides a preparation method of the cleaning agent for removing the emulsion deposits. The cleaning agent can effectively remove the emulsion deposits of a gathering and transportation systemand has the advantages that the formula is environmentally friendly, the usage amount is low, the cleaning effect is good, oil and water are separated after cleaning, and a using method is simple.