I want my application to be unsearchable from the App Store. I would like that only those users who sign in to my web site and then click the link of my iPhone application on app store, can install and use my application.
Is there any way to do that?
Your application will be found when they search for the name of the app or your name. There's no special option in iTunes Connect to hide your app.
While your application will be found when searched for, as long as it's not installed in large numbers, it won't show up in the top 50 lists. Which kind of is the same.
Tip: don't specify any keywords when registering your app, as these will improve the "searchability".
Edit: you might want to implement some kind of authentication in your app, so users who do have installed your app need to register first, before they can actually use it. Relying on your app not being found, isn't very "clean".
Not sure if this is going to work, but it may be worth a try:
You can set the release date of the application to the future. This removes the app from the catalog, which is a common way to remove an app temporarily (e.g. when it has problems) until an update appears.
However (this is possibly the catch) I don't know if the app will then be still available for sale via link or if the link will become unusable too.
The best bet is to use obscure keywords on submission along with an obscure app name.
Apple sells special developer licenses if you want to control the installation. They are meant for Enterprises to develop and deploy applications for only their use. Here's an article about it:
I think, without meaningful keywords your app should vanish amongst the 99.999 other apps.
As an alternative you could let everyone (search and) download the app and disable it until the user signed in.
You can also use in-house-distribution with the enterprise program (see here).