It has been known for decades that bone exhibits piezoelectric behavior. In recent years, it was directly proved that this effect stems from a polymeric matrix in bone, i.e., collagen fibrils. This effect in collagen is distinctly different from organic piezoelectric crystals, given the semicrystalline molecular structure of the collagen biopolymer. As such, the molecular mechanism of this electromechanical coupling effect in a realistic "super-twisted" model of collagen has been elusive. Herein, we present an investigation on the molecular mechanism of piezoelectric effect in collagen using full atomistic simulation based on the experimentally verified "super-twisted" microstructure of collagen. Our results reveal that collagen exhibits a uniaxial polarization along the long axis of the collagen fibril. In addition, the piezoelectric effect in collagen originates at the collagen molecule level and is due to the mechanical stress-induced reorientation and magnitude change of the permanent dipoles of individual charged and polar residues. A piezoelectric constant in the range of 1-2 pm/V (pC/N) is obtained from the simulation, which agrees well with the experimental data.