What is the correct form of the following ?
Look that from your own eyes ?
Look that in your own eyes ?
When used to talk about using your eyes, "look" is intransitive, meaning that it does not accept an object. You cannot say "he looks the apple". Instead you need to say that "he looks at the apple", where "at the apple" specifies the direction of looking.
Similarly, you have to say "Look at that with your own eyes.", where "with your own eyes" specifies the manner of looking. Also, if the object is near, you should say "Look at it with your own eyes.", because "that" tends to connote something not so near.
I would say "Have a look at it for yourself". "With your own eyes" sounds like an expression of a foreign language, but it doesn't sound English.