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Could a hacker, with your IP, session hijack you and remote control your desktop on Linux?

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Theoretically they could, if you have your computer set up to either allow Remote Desktop or SSH depending on which one you are asking about.

However they would need your IP address and your username. From this point they would have to brute force into your system if you have password authentication turned on. This can be mitigated by enabling Key Encryption instead of password authentication.

So yes they can but if your machine is running default settings and you are careful it will greatly mitigate the possibility of your machine being hijacked.

Basic Ubuntu Security Guide, Desktop Edition is a good read for information on Securing your Ubuntu machine.

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    Just to clarify Robby's excellent answer for less sophisticated users: The crucial part of Robby's answer is "if you have your computer set up to either allow Remote Desktop or SSH . . .". IP is not really a security issue in and of itself. That is a widespread misconception. It may be needed to exploit your system, but it isn't the only thing needed and not having it isn't the thing that stops people because it is normally easy to get. May 17 '17 at 17:33
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    It would also be important to note that if there are any 0-days out there to do with this sort of thing then vulnerabilities in really any internet facing application could cause this.
    – user364819
    May 17 '17 at 17:35
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    You give your IP to every website you visit. If you get email with enclosed pictures and you have it set to see those pictures (as opposed to text only) a clever black hat can get your IP and know when you open the email.). A black hat may care about exposing HIS IP, but it's a different issue. It isn't at all clear to me what OP means by "with your . . . session". May 17 '17 at 17:36
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    But a note of restrained optimism: In practice, so far, exploits of 'nix systems have been few and far between compared to Win. Win people like to claim that is because it is a much smaller user base, so not as good a target, which is nonsense imo. The user base is smaller but it is much higher value - most of the web runs on some kind on nix. In fairness to the Win crowd, part of why nixes get exploited less is simply because our percentage of really dumb users is much lower. May 17 '17 at 17:41

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