I see that History and His Story have the same way to read.How can we find the difference in these ways?

History sounds a little different because Du say "ery" at the end. Du actually hear the "or" in story

As poster above said. Most people pronounce history with an ending like "ery." Which is different than His Story. Not to mention in His Story there is a slight pause between His and Story. Whereas History there is no pause.
Plus Du can definitely tell Von content. The words might sound similar but they are nothing alike so there is really no way to confuse them in context.