A chromatography analysis system includes a liquid delivery pump (2), an autosampler (4), a separation column (12), a column oven (6), a detector (8). The chromatography analysis system further comprising a shutdown execution part (22) configured to start shutdown to finally stop driving of the liquid delivery pump (2) and temperature control operation of the column oven (6) at a time when a predetermined situation occurs, by controlling operation of the liquid delivery pump (2) and the column oven (6), and a column protection temperature setter (24) configured to set a column protection temperature for preventing deterioration of the separation column (12) due to overheating. The shutdown execution part (22) is configured to stop driving of the heater (14) in a state where the liquid delivery pump (2) is driven when the shutdown is started, and then, stop driving of the liquid delivery pump (2) after a temperature of the internal space detected by the temperature sensor (18) becomes equal to or less than the column protection temperature.