Disclosed is a novel long-acting glucagon conjugate in which glucagon or its derivative is covalently linked to a polymer carrier via a non-peptide linker, and a pharmaceutical composition comprising the same as an effective ingredient useful for the prevention and treatment of obesity. Since the long-acting glucagon conjugate of the present invention shows improved in vivo durability and stability, when used in combination with an anti-obesity drug, it is possible to induce synergistic effects on the loss of body weight and decrease in food intake without causing any side-effects such as fluctuation in blood glucose level. Accordingly, the long-acting peptide conjugate of the present invention is very effective for the prevention and treatment of obesity.