You can use SPE column to extract inorganic salts from the total methanolic extract. Also, I have noticed that methanolic extract will generate some crystals if you put them in -20C freezer for a while. I want to know whether that crystals are inorganic salts.

There shouldn't be a lot of those salts, unless the plant material contained a lot of water which was picked up by the methanol and carried the salts into the extract as well.

You can partition the extracted material in solvents of increasing polarity (hexane, ethyl acetate, dichloromethane), or desalt with a C18 or CHP20 column. Condition the column, dissolve the sample using the minimum amount of methanol, load the sample on the column, wash with water ( keep the washings in case your active compound is water soluble), then elute the column with methanol.