In this paper, a systematic design method for polarization-insensitive tunable liquid crystal (LC)-based metamaterial filter with the passband of flat-top and sharp roll-off is proposed. A compact LC-based bandpass metamaterial filter unit cell with a dimension of 0.09 lambda x 0.09 lambda is designed. The metamaterial filter element consists of a pair of planar pinwheel-shaped metallic structures with four symmetrically distributed isosceles triangular patches. LC is sandwiched in this pair of metallic structures. The metal pattern on each layer is 90 degrees rotationally symmetrical leading that the LC-based metamaterial filter is insensitive to the polarization of incident waves. In order to obtain the transmission characteristics of flat top and sharp roll-off, a double-layer LC-based metamaterial filter structure is proposed. Full-wave simulations show that the central frequency of the metamaterial filter is tuned from 10.88 GHz to 11.78 GHz, and the tuning range reaches up to 7.9%. Meanwhile, under TE and TM polarizations, the double-layer LC-based metamaterial filter structure achieves filtering characteristics with a flat-top passband of not less than 997 MHz and sharp roll-off for arbitrary LC states. Moreover a prototype sample is designed, fabricated, and measured to verify the proposed design method.