Cry, the Beloved Country is a social protest against the structures of the society that would later give rise to apartheid. Paton attempts to create an unbiased and objective view of the dichotomies this entails: he depicts the Whites as affected by 'native crime', while the Blacks suffer from social instability and moral issues due to the breakdown of the tribal system. It shows many of the problems with South Africa such as the degrading of the land reserved for the natives, which is sometimes considered to be the main theme, the disintegration of the tribal community, native crime, and the flight to urban areas.
Another prevalent theme in Cry, the Beloved Country is the detrimental effects of fear on the characters and society of South Africa as indicated in the following quotation from the narrator in Chapter 12:
Cry, the beloved country, for the unborn child that is the inheritor of our fear. Let him not love the earth too deeply. Let him not laugh too gladly when the water runs through his fingers, nor stand too silent when the setting sun makes red the veld with fire. Let him not be too moved when the birds of his land are singing, nor give too much of his heart to a mountain or a valley. For fear will rob him of all if he gives too much.
Paton makes frequent use of literary and linguistic devices such as microcosms, intercalary chapters and dashes instead of quotation marks for dialogue to indicate the start of speech acts in order to portray the devastating conditions in South Africa.