In a method of programming in a nonvolatile memory device including a memory cell region including a first metal pad and a peripheral circuit region including a second metal pad, wherein the peripheral circuit region is vertically connected to the memory cell region by the first metal pad and the second metal pad, a memory block in the memory cell region including a plurality of stacks disposed in a vertical direction is provided where the memory block includes cell strings each of which includes memory cells connected in series in the vertical direction between a source line and each of bitlines. A plurality of intermediate switching transistors disposed in a boundary portion between two adjacent stacks in the vertical direction is provided, where the intermediate switching transistors perform a switching operation to control electrical connection of the cell strings, respectively. A boosting operation is performed to boost voltages of channels of the plurality of stacks while controlling the switching operation of the intermediate switching transistors during a program operation with respect to the memory block. Program voltage disturbance and pass voltage disturbance are reduced through control of the switching operation of the intermediate switching transistors.