A highly integrated programmable non-volatile memory and a manufacturing method thereof are provided. More particularly, a memory device including an antifuse and a diode, or a variable resistor and a diode, an operation method thereof, and a manufacturing method of a plurality of memory cells capable of increasing the integration density by utilizing a vertical space are provided. The highly integrated programmable non-volatile memory includes first stepped cells and second stepped cells formed to have different heights. The first stepped cells are formed on a horizontal plane with a high height, and the second stepped cells are formed on a horizontal plane with a low height.