In the Novel Series Blair is very possessive of Nate, she has always worried about Serena's hold on him so when her best friend left for boarding school she was pleased to have her out of the way. Nate, on the other hand is tired of waiting for Blair to be ready to sleep with him and often finds her to be clingy.
They dated on-off for the first few books before breaking up in Nobody Does it Better when Blair walked in on Nate and Serena having sex. This was a blow for her because it had only been a few weeks since she had first lost her virginity to Nate.

Nate and Serena's affair caused Blair to be on the warpath once again, however it is shown in 'Only in Your Dreams' that Nate still has feelings for Blair.

In Only In Your Dreams, Blair forgives Serena and Nate for sleeping together, as she has found a new boyfriend, Lord Marcus. This upsets Nate because he is still in love with Blair, and the only reason he and Serena were dating was to make it seem as if they weren't just random hook-ups.

In Would I Lie To You, Blair and Serena move into a house in the Hamptons which just so happens to be right next to Nate's. When Nate comes over, and he finds out things between Blair and Lord Marcus didn't work out, he tries to get her back. After Blair realized she was also in love with Nate, they stay together, and on Serena's birthday, leave town to go on Nate's boat and take a three month cruise