Visible-light color filters using patterned nanostructures have attracted much interest due to their various advantages such as compactness, enhanced stability, and environmental friendliness compared with traditional pigment or dye-based optical filters. While most existing studies are based on planar nanostructures with lateral variation in size, shape, and arrangement, the vertical dimension of structures is a long-ignored degree of freedom for the structural colors. Herein, we demonstrate a synthetic platform for transmissive color filter array by coordinated manipulations between height-varying nanocavities and their lateral filling fractions. The thickness variation of those nanocavities has been fully deployed as an alternative degree of freedom, yielding vivid colors with wide gamut and excellent saturation. Experimental results show that the color-rendering capability of the pixelated nanocavities can be still retained as pixels are miniaturized to 500 nm. Crosstalk between closely spaced pixels of a Bayer color filter arrangement was calculated, showing minimal crosstalk for 1 m square subpixels. Our work provides an approach to designing and fabricating ultracompact color filter arrays for various potential applications including stained-glass microprints, microspectrometers, and high-resolution image sensing systems.