The invention discloses a compartment air-conditioning zoning controlling system for ships and a controlling method thereof. The controlling system comprises a central control box and a central control system, wherein the central control system comprises a new air and return air mixed cabin which is used for receiving new air, simultaneously receiving return air which is exhausted from a pluralityof cabins, and mixing the fresh air with the return air to obtain mixed air; a primary cooling-heating medium water temperature controlling system which is used for receiving the mixed air and carrying out primary temperature adjustment of the mixed air, a secondary cooling-heating medium water temperature controlling system which is used for receiving the mixed air and carrying out secondary temperature adjustment of the mixed air, and a post-treatment and pressurizing system which is used for receiving the mixed air and carrying out post-treatment and pressurization on the mixed air, wherein the mixed air which is processed by adopting the post-treatment and pressurizing system is exhausted into the plurality of the cabins. According to the controlling system provided by the invention,temperature zoning of the compartment air-conditioning system is controlled, so that needs of thermal comfort levels for different people can be met, electric load of a whole-ship air conditioning system is reduced, and configuration requirements of power generators for the ships are reduced.