The invention discloses an electrochemical air conditioning system and a control method, and belongs to the field of air conditioners. According to the electrochemical air conditioning system, a firstintercepting pipeline is connected between an outflow pipeline and a backflow pipeline of a first hydrogenated metal heat exchanger, a second intercepting pipeline is connected between an outflow pipeline and a backflow pipeline of a second hydrogenated metal heat exchanger, and a cold and hot neutralization pipeline set is connected between the first hydrogenated metal heat exchanger and the second hydrogenated metal heat exchanger. According to the system, a switching signal is added between two continuous hydrogen reversing switching signals to carry out a heat neutralization mode, the first hydrogenated metal heat exchanger and the second hydrogenated metal heat exchanger are subjected to heat neutralization before cold and hot alternation so as to be prevented from changing from extreme hot into extreme cold, or from the extreme cold into the extreme hot, and the service life of a electrochemical compression refrigerating device is prolonged; in addition, the refrigeration mode or the heating mode can be kept after an electrochemical device stops running, comfortable cold air or hot air is blown out, the comfort and the stability are improved, and useless work is reduced.