I would say that the main theme present throughout the novel is love and many of the sub-themes associated with love. Love as a uniting power. Love as something that transcends time. Love at first sight.
The love story that is woven throughout the entire novel is the love between Marco and Celia. What's great about their love is that the two of them are more or less in love before they even meet. Each of them mystically creates and controls the Night Circus. Their mentors intended the circus to be a competition between the two of them, but Celia and Marco use their circus inventions as a way to court each other. By the time that they actually meet and realize who the other person is, there is no question that they will be in love with each other.
Their love transcends time. As long as the two of them are involved with the circus competition, the circus and its workers do not age. Celia's and Marco's love for each other really is eternal at that point. Their love is also the power that is holding everything together for much of the story.
A second main theme is the theme of family. The Night Circus changes this theme a little bit, because the theme is not bound to blood relations. There are two main families in the book that provide support for their family members. The first family is the circus performers. They are a tight knit group that actively protects and supports each other. The other family is the Reveurs. Essentially, they are a fan club of the circus. But they are much more than a fan club. They loan each other houses, financially support group members as needed, and help each other in any means possible. This is very evident when the Reveurs take Bailey under their wing and work very hard to get him to the Night Circus in order to take over its governance.