It means arithmetic. "The Three R's" is a joking way of referring to the most basic school subjects -- "reading, 'riting (writing) and 'rithmetic (arithmetic)." There's an old song that refers to "reading and 'riting and 'rithmetic, taught to the tune of a hick'ry stick." (Long ago, a teacher might have hit unruly students with a hickory stick to discipline them.)
(Arithmetic refers to basic math skills -- addition, subtraction, multiplication and division.)