The invention discloses a flexible minimally invasive surgery instrument based on a natural orifice. The flexible minimally invasive surgery instrument comprises an operation handle, a wrist driving device, a connecting catheter, a flexible wrist part and a tail end executing device. The flexible minimally invasive surgery instrument can be integrally applied to minimally invasive surgery in the fields of abdominal cavity, thoracic cavity, urination, gynecology and the like. In the surgery implementation process, the minimally invasive surgery intelligent instrument passes through a trocar hole formed in the body surface of a patient, and a doctor holds the instrument by hand, and puts the instrument into the body to implement the surgery operation; the instrument is held by the doctor by hand; all operations, including the instrument tail end opening and closing movement, of an ordinary minimally invasive surgery instrument can be realized; meanwhile, the three-freedom-degree movement (the pitching movement, the swinging movement and the auto-rotation movement) of the tail end of the instrument can also be realized through controlling the operation handle and the wrist driving device. The space multi-freedom-degree surgery actions can be output by the instrument, the action is flexible, and the operation force is great; the instrument is more suitable for minimally invasive surgery with complicated actions.