The terahertz filters with multi-layered metamaterials are proposed and fabricated with the negative photoresist as isolation layer. The influence of the relative positions between the different layers to the electromagnetic resonance is discussed by experiment, which reveals that filter frequency is strongly related to the coupling between the different layers. The reason of the influence is theoretically analyzed by built the equivalent LC model. The work provides a good reference in the research of multi-layered terahertz metamaterials.