I am a non-resident alien who uses W2 form to file my taxes. Now I have a new job asking me to use 1042-s. If I file my tax next year do the IRS asked 1042S on my other job? Or can I file W2 and 1042S together?

Yes, you must report all your income.
Read: Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents (http://taxipay.blogspot.com/2008/03/us-tax-filing-requirements-for-non.html)