Our Web application is based on IE9, which means only IE9 can open the pages in our site. We\'ll prevent user to browse our site when their browser is not IE9. But sometime
It sounds like you want to have a link in an email that activates a specific program on the user's computer rather than the program that they've identified should be used (e.g., their default browser). I don't believe you can do that.
You can install "protocol handlers" in both Chrome and Safari (I suspect Firefox as well), which would let you send a link like ie://example.com/path/to/app. Your protocol handler would launch IE and take you to the relevant site. (Apple does this with iTunes.) But your users would have to install the handler (and, of course, you'd have to write it).
An easier answer might be to have the users install any of the ubiquitous "open in IE" add-ons/extensions that exist for Chrome, Firefox, etc. They follow the link, then choose "open in IE" from some kind of menu. (If they're using webmail, they may even be able to right-click the link and choose that line item, depending on the extension.)
Side note: Obviously, though, barring it being impossible I'd recommend making your application compatible with Chrome and Firefox.