My father has visa till July 2016, and when we came to US in March 2016, immigration officer put date of Sept 2016.
Now, I have to know that, can he stay till Sept 2016, or he has to leave US before July 2016?
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He can stay until September. The visa expiration date is the date by which one must enter the US. See, for example, https://travel.state.gov/content/visas/en/general/visa-expiration-date.html.
Admission to the United States and your Duration of Stay
Upon arriving at a port of entry, the CBP official will determine the length of your visit.
On the admission stamp or paper Form I-94, the U.S. immigration inspector records either an admitted-until date or "D/S" (duration of status). If your admission stamp or paper Form I-94 contains a specific date, then that is the date by which you must leave the United State. If you have D/S on your admission stamp or paper Form I-94, you may remain in the United States as long as you continue your course of studies, remain in your exchange program, or qualifying employment. The admitted-until date or D/S notation, shown on your admission stamp or paper Form I-94 is the official record of your authorized length of stay in the United States. You cannot use the visa expiration date in determining or referring to your permitted length of stay in the United States.
Note the last two sentences: "The admitted-until date ... shown on your admission stamp ... is the official record of your authorized length of stay in the United States. You cannot use the visa expiration date in determining .. your permitted length of stay in the United States.
Reading between the lines, you may conclude that this is designed to stop people who have, for example, a 10-year visitor visa from claiming that they are authorized to stay in the US for 10 years. But it is equally true in your father's case, where the admitted-until date is later than the visa expiration date.