The invention relates to a method for evaluating the single event functional interrupt cross section based on a particle filter model, which is implemented according to the steps of carrying out a heavy particle accelerated irradiation test, calculating the average ion fluence rate L0 of each functional interrupt and the average accumulated irradiation total fluence N0 of each functional interruptunder the ion irradiation corresponding to a value LET0, and taking the calculated data as reference data; meanwhile, calculating the average upset bit number in the average test by using the configuration of a memory block read-back mechanism, and recording the number as i0; assuming that the heavy ion fluence rate of the irradiation test is L1 at a pre-estimated value LET1, building a particlefiltering model, predicting an expected number i with a tilde thereon of the SEU occurrence frequency; defining an equivalent functional coupling factor of the system to be [lambda], wherein [lambda] represents the probability of causing a function error of the system when any single-bit upset occurs in the system; carrying out equivalence on the system functional interrupt cross section [Sigma]sys according to the definition of [lambda]; and evaluating the system functional interrupt cross section in the case of unknowing the value of LET1 according to the predicted expected value iwith a tilde thereon of the SEU occurrence frequency and the reference data.