The invention discloses a medical device rust removing agent. The medical device rust removing agent comprises, by mass percent, 5%-50% of organic acid, 5%-30% of a surface active agent, 5%-15% of a corrosion inhibitor, 5%-10% of a solvent, 1%-10% of a bactericide, 0.01%-1% of essence and the balance pure water, and the total amount is 100%. According to the medical device rust removing agent, the new corrosion inhibitor is used as a raw material for preparing the rust removing agent, the beneficial effects that efficient corrosion inhibition and scale inhibition and chelation are achieved, no toxin exists, and rinsing is easy are achieved, rust removing is conducted efficiently, and a device can also be effectively protected. The preparing method is simple, the performance is reliable, environment friendliness is achieved, no toxin, harm and pollution exist, and the medical device rust removing agent is ideal.