The phrase you cite shows up in the first chapter of the book. There, Orwell says that the essential crime that contains all others is thoughtcrime.
Winston knows as soon as he writes anything in his diary that he has committed thoughtcrime. But he also realizes that even if had not written a word that he still would have committed thoughtcrime just in thinking the words "Down with Big Brother."
I believe that this is the essential crime because it involves a rebellion against what the Party wants. There is nothing that is worse than that.