The invention provides a process for separating calcium and magnesium ions from waste water containing manganese. The process comprises the following steps: mixing fluoride which is a precipitating agent with waste water containing manganese through a form of dry powder feeding, generating sediment after a full reaction, carrying out press filtration on sediment slurry with a plate and frame filter press, and followed by clear liquid filtering to enters subsequent processing. Processing equipment of the process comprises a precipitating agent bunker, a dry powder feeder, a reaction tank, a sedimentation basin, a clear liquid pool, an ultrafiltration system and the plate and frame filter press, wherein a stirrer is provided with in the reaction tank, and pipelines and pumps are provided between equipment. The advantages of the process in the invention are as follows: the process is suitable for processing waste water containing manganese with various ion concentration, and application range of pH value of the process is wide; the process has a high rate of calcium and magnesium ions removal, and through adjusting addition a removal rate can reach 100%; on condition that a loss rate of manganese ion is less than 0.2%, the process can effectively remove the calcium and magnesium ions from the waste water containing manganese to achieve the purpose of separating calcium magnesium ions. The process is suitable for separating calcium and magnesium from waste water in electrolytic manganese production.