The invention discloses a three-dimensional simulation culture system for stem cells, and belongs to the technical field of biology. The invention solves the problems of complex operation, low efficiency, small yield and poor quality in an existing in-vitro culture of stem cells. The three-dimensional simulation culture system for the stem cells comprises a stem cell nest, a heart region first peristaltic pump, a lung region, a kidney region, a spleen region, a stomach region, a liver region, a first fluid pressure gauge, a first pressure regulating valve, a liquid level meter, a three-way valve, a first control valve, a temperature regulator, a thermometer, an oxygen/carbon dioxide measuring instrument, a PH measuring instrument, a nutritional ingredient measuring instrument, a second control valve, a second peristaltic pump, a third peristaltic pump, a urea/uric acid/inorganic salt measuring instrument, a fourth peristaltic pump, a third control valve, a second fluid pressure gauge,a second pressure regulating valve, a fourth control valve, a fifth control valve, a fifth peristaltic pump, a sixth control valve, a gas permeable membrane, a dialysis membrane, a central control platform, a cloud data center and an electromagnetic field. According to the three-dimensional simulation culture system for the stem cells, the stem cells with higher quality and quantity can be cultured, the stability is good, and the treatment effect of the stem cells is improved.