A preparation system of a diester-based composition, the system comprising: a first purification part comprising a purification space for separating a reaction product of esterification reaction of a dicarboxylic acid and a first alcohol into a purified product and the first alcohol which is an unreacted reactant, and a purified product line and an unreacted reactant recovering line for discharging the purified product and the unreacted reactant; a trans reaction unit comprising an interior space for performing trans esterification reaction of the purified product injected from the purified product line of the first purification part and a second alcohol injected from a separate alcohol injection part, and a trans reaction product line discharging a produced trans reaction product; a neutralized water separating apparatus comprising a partition wall separating an interior part into a neutralization space and a water separation space and forming a passage capable of moving a fluid, and an organic layer line and a waste water line for separately discharging an ester-rich organic layer and a water-rich waste water layer from the water separation space, the trans reaction product line being connected with the neutralization space; a second purification part comprising an unreacted reactant recovering line, a second waste water line and a product line for separately discharging the ester-rich organic layer injected from the organic layer line of the neutralized water separating apparatus into three streams of a mixed alcohol of the unreacted first alcohol and the second alcohol, a mixed waste water comprising water, the first alcohol and the second alcohol, and a diester-based composition; and a waste water treating unit comprising a waste water injecting line which is connected with the waste water line of the neutralized water separating apparatus and the second waste water line of the second purification part, an extracting agent injecting line injecting the first alcohol which is an extracting agent, a layer separating space for layer separating a mixed waste liquid of water, the first alcohol and the second alcohol into a mixed alcohol layer and a waste water layer, and a mixed alcohol recovering line and a final waste water line, separately discharging the mixed alcohol layer and the waste water layer. a first purification part comprising a purification space for separating a reaction product of esterification reaction of a dicarboxylic acid and a first alcohol into a purified product and the first alcohol which is an unreacted reactant, and a purified product line and an unreacted reactant recovering line for discharging the purified product and the unreacted reactant; a trans reaction unit comprising an interior space for performing trans esterification reaction of the purified product injected from the purified product line of the first purification part and a second alcohol injected from a separate alcohol injection part, and a trans reaction product line discharging a produced trans reaction product; a neutralized water separating apparatus comprising a partition wall separating an interior part into a neutralization space and a water separation space and forming a passage capable of moving a fluid, and an organic layer line and a waste water line for separately discharging an ester-rich organic layer and a water-rich waste water layer from the water separation space, the trans reaction product line being connected with the neutralization space; a second purification part comprising an unreacted reactant recovering line, a second waste water line and a product line for separately discharging the ester-rich organic layer injected from the organic layer line of the neutralized water separating apparatus into three streams of a mixed alcohol of the unreacted first alcohol and the second alcohol, a mixed waste water comprising water, the first alcohol and the second alcohol, and a diester-based composition; and a waste water treating unit comprising a waste water injecting line which is connected with the waste water line of the neutralized water separating apparatus and the second waste water line of the second purification part, an extracting agent injecting line injecting the first alcohol which is an extracting agent, a layer separating space for layer separating a mixed waste liquid of water, the first alcohol and the second alcohol into a mixed alcohol layer and a waste water layer, and a mixed alcohol recovering line and a final waste water line, separately discharging the mixed alcohol layer and the waste water layer.