The invention discloses a method for detecting ionized layer TEC exception. The method comprises the following steps of: A, performing smoothing filtration on an ionized layer TEC time sequence; selecting the TEC time sequence of any point according to the space-time characteristics of ionized layer TEC distribution, and performing smoothing filtration on the ionized layer TEC time sequence by adopting a moving average method to obtain a smoothed TEC time sequence; B, calculating a difference between a TEC smoothing value and an observation value so as to obtain a time sequence of a smoothed residual error; C, determining the arc length of a sliding window, calculating a mean value and a standard difference, adding 2 times standard difference to the mean value to obtain an upper limit value, subtracting 2 times standard difference from the mean value to obtain a lower limit value, performing exception detection on the time sequence of the residual error, comparing the data with the upper limit value and the lower limit value, and judging that the data between the upper limit value and the lower limit value is normal; and D, storing the detection result. The method is simple, has obvious effect, creatively performs the exception detection of the ionized layer TEC based on the smoothed residual error data, deducts the long periodic tendency of the TEC, and greatly improves the reliability of the detection result.