The biggest difficulty of this battle is that Mister Freeze will become immune to any attack you use after the first try. Therefore you will need to use five different tactics against him, as that's the amount of attack you need to perform on him to win.
You should perform the first attack right after the battle begins. It implies using the Disruptor, so obviously you need to equip it. Quickly aim at Freeze and disrupt his freeze gun #1. Afterwards run to him and start leading out fast attack with the Beat down skill by rhythmically pressing X #2.
Before you do anything more, dedicate some time to analyze Mister Freeze's skills. He will be walking through the room and using his freeze gun whenever he sees Batman #1, therefore you should often use Detective Mode to watch his movements. Apart from that Freeze will launch guided ice projectiles from time to time #2. The attack is best avoided by hiding inside one of the rooms on the bottom level. Also do note that you can't use any vantage points. Therefore the whole battle is best played while staying on the ground, maybe using the Grapnel Gun just to quickly reach the side balconies.
The second attack implies attacking him by surprise. Turn on Detective Mode and use it to quietly get behind Mister Freeze's back #1. Approach him, press Y #2 and afterwards quickly approach him once again and this time start pressing X rhythmically.
The third attack implies surprising Mister Freeze by attacking from one of the grates in the floor #1. Hide inside one of them, wait for Freeze to get nearby and press Y #2. It's also worth to notice that is Freeze fires the guided projectiles, they can find Batman inside the shaft and damage him. In such situations you should quickly get out and hide inside one of the side rooms. After performing the attack, be sure not to forget about the finishing move (pressing X).
The fourth attack is best led in the western room on the lowest level. Place yourself beside the big red button #1 and wait for Freeze to come. When he comes and stops on the flooded part of the floor, press the button to zap him with electricity #2. Just like before, approach him and start attacking by pressing X.
The last, fifth attack implies using the Electrical Charge. Find one of the generators in the room, hide inside the northern room, aim at it #1 and wait for Freeze to come. Send a charge and note that the discharge has worked on the boss #2. Of course attack him (X).
If the above attack was the fifth one, you will now have to finish off Freeze for good by pressing X #1. Winning the battle will start another cutscene, during which Harley Quinn will take advantage of the situation and steal the cure. As a compensation, Freeze will give you a new gadget - the Freeze Blast #2.