You can not access to the users SMS inbox, this would be a real privacy issue.
What you can do is register your own app schema, with your app can be opened. The you can do something like myApp://register/<OTP>
, you can then pick up this URL and take the OTP from the URL and use it. Just use the URL in your SMS and iOS will do the rest.
You can parse the app URL in - (BOOL)application:(UIApplication *)application openURL:(NSURL *)url sourceApplication:(NSString *)sourceApplication annotation:(id)annotation
in your app delegate.