The invention discloses a pre-estimating method for a single event effect cross section of an anti-irradiation integrated circuit, wherein the method mainly settles a problem of single event effect cross section pre-estimation in the same ground heavy ion acceleration irradiation experiment condition. The pre-estimating method is characterized in that based on a high volume of engineering experiment data, logical relevance between a total ion injection amount and the number of single event effects caused by the ions is analyzed; and according to a single event effect generating mechanism and a statistical theory of probability, a pre-estimating model for a time node [delta]ti+1 when the next single event effect occurs and a pre-estimating model for a whole circuit single event effect cross section delta are established, thereby establishing a logical relation between the total ion injection amount and the number of the caused single event effects. The pre-estimating method settles the problem of single event effect cross section pre-estimation in the same experiment condition and supplies an engineering analysis facility for ground acceleration simulation experiment evaluation for the anti-irradiation integrated circuit. The pre-estimating method can be used for pre-estimating irradiation resistance of a spaceflight microelectronic device.