A method for separating and preparing a pearl extract from pearls comprise the following steps: 1) pulverizing pearls to a nanometer scale, then adding deionized water, and micro-emulsifying pearl powder by means of cooperation of a pressure and a temperature; 2) then performing electrodialysis on a pearl powder emulsion, placing the deionized water in a concentrated water pool, placing the pearl powder emulsion in a fresh water pool, and performing cyclic decalcification and separation to obtain a calcium salt-containing solution and a pearl protein solution; 3) using the obtained calcium salt-containing solution as soluble edible calcium or a soluble edible calcium raw material; 4) adding a phosphate buffered saline into the obtained pearl protein solution to form a homogeneous mixture; and 5) first performing pre-processing, then placing the liquid mixture into a reaction vessel to carry out an enzyme-catalyzed reaction, killing enzyme in a boiling water bath centrifugally after the reaction finishes, and removing a supernatant liquid, namely, a pearl complex whitening factor solution