Observe pulse electromagnetic fields (PEMFs) effects on ovariectomized (OVX) rats, to study the mechanisms of PEMFs therapy for postmenopausal osteoarthritis. Forty-eight female rats were exposed to PEMFs (PEMFs group), administrated E2 and placebo PEMFs (E group), or were treated with placebo PEMFs (OVX and Sham groups). The treatment duration was 30 days after which serum E2 levels, chondrocyte morphology, chondrocyte apoptosis and matrix metalloproteinases-13 expression in knee joint was analyzed. We observed differential chondrocyte formation in each group, and serum E2 content in the PEMFs and E group were significantly higher than the OVX group. The apoptosis index of chondrocytes and the positive index of MMP13 expression in the PEMFs group and E group were significantly lower than the OVX group. PEMFs has a systemic effect on estrogen metabolism in ovariectomized rats, then inhibit chondrocyte apoptosis and downregulate MMP13 expression of knee joint cartilage. It may be the mechanisms by which PEMFs therapy works for on postmenopausal osteoarthritis.