A manufacturing method of a MEMS sensor includes a step of, by irradiating a first hole formed in a second layer on a semiconductor substrate with a focused ion beam for a first predetermined time, forming a first sealing film, which seals the first hole, on the first hole, and a step of, by irradiating a second hole formed in the second layer with a focused ion beam for a second predetermined time, forming a second sealing film, which seals the second hole, on the second hole. At this time, each of the first predetermined time and the second predetermined time is a time in which thermal equilibrium of the second layer is maintainable, and the step of forming the first sealing film and the step of forming the second sealing film are performed repeatedly.