A vertically integrated waveguide self-coupled resonator based tunable optical filter was demonstrated. Unlike the conventional U-bend self-coupled waveguide structure, a top-layer S-bend waveguide was cross-coupled with the racetrack resonator on a bottom layer. The different waveguide coupling effect was compared with the same resonance structure, which can realize the same free spectral range as well as a high quality factor. Spectrum response can be designed separately by varying the coupling coefficient between waveguide and resonator. A heater attached on the top of the resonator can be utilized for the resonance wavelength tuning, while a heater on the top of cross-coupled waveguide has little influence on the device performance, which can help to improve the stability. The presented device can also be applied as a tunable modulator/switch.