It is theoretically established that self-fertilization can facilitate mutation accumulation, thus increasing extinction risk. However, in previous studies, selfing rates are often set as fixed parameters, but in natural systems, evolution of selfing rates and deleterious mutations may mutually affect each other. I carried out simulations to investigate the dynamics of selfing rates and mutation accumulation, by allowing deleterious mutations to coevolve with alleles that modify the selfing rate (selfing modifiers). I found that selfing rates will often fluctuate over time, due to successive invasion of alleles that increase selfing and outcrossing. Since mutation fixation is mainly caused by Muller’s ratchet, its rate is sensitive to the change of the selfing rate mutations will accumulate in a punctuated pattern. The dynamics are influenced by several factors, such as recombination and the selfing rate effects of selfing modifier loci. Also, such temporal variation produces variation of selfing rates and mutation accumulation rates between multiple conspecific populations, which can increase the average fitness across populations. As factors, such as the genomic mutation rate of deleterious mutations, can simultaneously influence the selfing rate and mutation fixation, effects of these factors on mutation accumulation rates can be complicated and non-monotonic.