Without a lot more information, it's hard to give a good answer to this question. Adding two-factor authentication to an application of course depends on a lot of things. What programing language are you using? Are you using any frameworks like Django or Rails?

If you are using Python and Django, django-otp or django-two-factor-auth are probably good starting points. If you are using Ruby on Rails, there are a number of gems that build on top of Devise to do two-factor auth. Twilio has some great tutorials on the subject in a variety of languages.