A method of operating a nonvolatile memory device that includes a three-dimensional (3D) memory cell array is provided as follows. A first read operation is performed on first memory cells connected to a first word line by using a first read voltage level. A read retry operation is, if the first read operation fails, performed on the first memory cells so that a read retry voltage level is set to a second read voltage level. A read offset table is determined based on a difference between the first read voltage level and the second read voltage level. The read offset table stores a plurality of read voltage offsets. A second read operation is performed on second memory cells connected to a second word line by using a third read voltage level determined using the read offset table.