Aluminum nitride (AlN) piezoelectric thin films with c-axis crystal orientation on polymer substrates can potentially be used for development of flexible electronics and lab-on-chip systems. In this study, we investigated the effects of deposition parameters on the crystal structure of AlN thin films on polymer substrates deposited by reactive direct-current magnetron sputtering. The results show that low sputtering pressure as well as optimized N2/Ar flow ratio and sputtering power is beneficial for AlN (002) orientation and can produce a highly (002) oriented columnar structure on polymer substrates. High sputtering power and low N2/Ar flow ratio increase the deposition rate. In addition, the thickness of Al underlayer also has a strong influence on the film crystallography. The optimal deposition parameters in our experiments are: deposition pressure 0.38 Pa, N2/Ar flow ratio 2:3, sputtering power 414 W, and thickness of Al underlayer less than 100 nm.