We report Raman spectroscopic investigation of pressure induced changes in nano-crystalline Cu2ZnSnS4 (grain size ~14 nm) synthesized by microwave method. Raman scattering measurements carried out at high pressures up to 23.5 GPa revealed an interesting sequence of phase transitions; different from the behaviour of bulk Cu2ZnSnS4 reported earlier. At around 9 GPa, the compound transformed from the ambient ordered kesterite phase to a disordered kesterite structure which showed signatures of instability with further pressurization. The compound transformed to a new phase above 23 GPa (probably rock-salt phase), suggesting that properties of nanocrystalline Cu2ZnSnS4 are quite different from that of bulk Cu2ZnSnS4. Both the phase transitions are completely reversible. High pressure synchrotron powder diffraction measurements performed up to 12.1 GPa also confirm the transition from ordered kesterite to disordered kesterite structure above 9 GPa. The equation of state data for the ordered kesterite phase is obtained. Anomalous behavior of the Raman modes in the disordered kesterite phase indicates mechanical instability which leads to the second structural transition. Present work provides stability regime of kesterite phase of nanocrystalline Cu2ZnSnS4 which is essential for its application as a solar cell absorber material.