Mr.A is the CEO of the company. Mr. B will be in charge when Mr. A is away for vacation, business trip, or etc. Is there a word or prefix to call Mr. B, for example, temporary CEO, acting CEO?
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I would use "acting CEO", or in a very formal or serious situation (grave illness, maybe): "CEO pro tem" (short for pro tempore, i.e. for the time being).
If you're looking for a word which can describe the person's role (not title) as a backup to the boss, whether or not the boss is currently absent, then as @Jaydles suggested in the comments, you can say "he is on standby"; alternatively you could say exactly backup or the more formal understudy (typically reserved for acting/theatre).
For example: "The boss' wife is going to give birth any day now, so he's got Sam on standby for him" (or just "Sam is on standby"), or the boss could say "Bob's my backup in case I have to leave early" or "Umberto is understudying me [or is my understudy]".
My suggestion for temporary CEO is Interim CEO
You could, especially in British English, refer to such a person as a locum, short for locum tenens, "one holding a place".