Portable or even on-chip detection of methane (CH4) is significant for environmental protection and production safety. However, optical sensing systems are usually based on discrete optical elements, which makes them unsuitable for the occasions with high portability requirement. In this work, we report on-chip silicon-on-insulator (SOI) waveguide CH4 sensors at 3.291 μm based on two measurement schemes including direct absorption spectroscopy (DAS) and wavelength modulation spectroscopy (WMS). In order to suppress noise, Kalman filter was adopted in signal processing. By optimizing the waveguide cross-section structure, an etch depth of 220 nm was selected with an experimentally high power confinement factor (PCF) of 23% and a low loss of only 0.71 dB/cm. A limit of detection (LoD) of 155 parts-per-million (ppm) by DAS and 78 ppm by WMS at an averaging time of 0.2 s were obtained for a 2 cm-long waveguide sensor. Compared to the chalcogenide (ChG) waveguide CH4 sensors at the same wavelength, the reported sensor reveals the minimum waveguide loss and the lowest LoD. Therefore the SOI waveguide sensor has the potential of on-chip gas sensing in the mid-infrared (MIR) waveband.