The invention discloses a method of harmlessly treating electrolytic manganese residue percolate, characterized by comprising the steps of 1), percolating electrolytic manganese residue percolate collected in a residue storage to obtain clarified filtrate; 2), adding saturated clarified limewater in a container of the clarified filtrate, and adjusting pH of a solution to 7.0-8.0 to obtain mixture A; 3), adding sodium silicate powder into the mixture A, and stirring for 1-2 hours to obtain mixture B, wherein a weight-volume ratio (g:mL) of the sodium silicate to the clarified filtrate of step 1) ranges from 1:150 to 1:200; 4), adding sodium chloride crystal into mixture B, and stirring to obtain mixture C, wherein sodium chloride concentration in the mixture C ranges from 200 mg/L to 250 mg/L; 5), adding a positive plate and a negative plate into a container of the mixture C, loading an electric field, and stirring for 3-4 hours to obtain the electrolytic manganese residue percolate that is harmlessly treated, wherein voltage of the electric field is 10-20 V.