A memory apparatus, a controller, and a method thereof for programming non-volatile memory cells are provided. The memory apparatus includes a plurality of memory cells, wherein each memory cell shares a source/drain region with a neighboring memory cell. The method utilizes a compensation electron flow applied into a source/drain region between two memory cells to provide enough electron flow to program one of the two memory cells, even under the circumstances that the other memory cell has a greater threshold voltage, such that the dispersion of the programming speed of the memory cells is reduced.