The present invention relates to a food composition for improvement and prevention of estrogen deficiency, the composition containing a thistle extract or a thistle and thyme complex extract as an active ingredient. The present invention has advantages of alleviating estrogen deficiency in climacteric women and improving symptoms caused by estrogen deficiency, such as facial flushing, sweating, fatigue, anxiety, depression, memory impairment, insomnia, increased blood cholesterol, weight gain, and reduced bone density.