The theme in The Thornbirds is complex. The novel spans across three generations of a family, and deals primarily with the restrictions placed upon women in society. The emphasis is women who have little freedom and are dependent on man. In essence, women during the time period of the novel, 1915-1969, had little options without men.
In addition, the novel deals with forbidden love, as third generation Maggie falls in love and has an illegitimate child with a priest, Ralph de Bricassart. It explores ambition, lies, and imperfection in a world of religious morality. Maggie unhappily marries while still desiring Ralph, as Ralph does her. But because of Ralph's ambition to further his career and the position he holds, they are torn apart left only with the burning desire of love for each other.
So to summarize, the themes deal with forbidden love and the sacrifices made in the name of love, ambition and power, and the oppression of women to choose and be what they want.