Q:

Can the main conflict be the inner conflict? 

I've recently been having trouble with developing plots.  The plots I created seemed heavily sequential.  No matter how many twists or complications I put in, they always seemed dry, proceeding from one problem to the next.  
I believe I have discovered a way to fix this: by making sure, from the beginning, that my conflict is linked to the theme, or message, of my novel.  In addition, I link the main character to the theme.  This seems to be working, and has the added benefit of acting as a safeguard against accidental preaching of said theme.  
HOWEVER, it appears that this method is prone to making the hero's inner conflict (what I think of as conflicting sides within the protagonist) be the MAIN conflict (the main problem in the story).  The main conflict is the inner conflict.  
Is this okay?  This doesn't strike me as much of a problem, but being an aspiring author, I want to be sure.   

A:

It depends on the genre and what you're trying to achieve, but it's certainly an accepted literary tool.  The good ol' Man vs Self conflict. 
It'll almost certainly result in a character-driven novel, but there's nothing wrong with character-driven novels! 

A:

It's totally okay, and makes for a nice vehicle of the theme (the plot itself is the deepest, subtlest and thus most effective means of making argument, as opposed to say the dialogue/opinions of your characters). 
But you shouldn't worry about whether or not it's arbitrarily "okay".  Hesitation holds new writers back, and one of the quickest ways to develop as a writer (and maybe even innovate your form) is to discard your fear of "breaking the rules".  Could Joyce have written Ulysses if he were afraid of doing something "wrong" like this?  Could Cortázar have written Rayuela?  
My advice (and this is advice given to scientists and mathematicians, too): trust yourself.  You are a human; you have experiences that others can empathize with, and you have messages you wish to send.  If you have a new idea for how to tell a story that hasn't been done before, you should be all the more excited to try it out first. 
Good luck! 
EDIT
Popular example of a novel driven by a character's inner conflict: Moby Dick.  If it worked for Melville, it can work for you!