Onboard signal processing system for infrared sensors has been developed for HAYABUSA2 for the exploration of C class near-Earth asteroid 162173 (1999JU3), which is planned to be launched in 2014. An optical navigation camera with telephoto lens (ONC-T), a thermal-infrared imager (TIR), and a near infrared spectrometer (NIRS3) have been developed for the observation of geology, thermo-physical properties, and organic or hydrated materials on the asteroid. ONC-T and TIR are used for those scientific purposes as well as assessment of landing site selection and safe descent operation onto the asteroid surface for sample acquisition. NIRS3 is used to characterize the mineralogy of the asteroid surface by observing the 3-micron band, where the particular diagnostic absorption features due to hydrated minerals appear. Since the processing cycle of these sensors are independent, data processing, formatting and recording are processed in parallel. In order to provide the functions within the resource limitation of deep space mission, automatic packet routing function is realized in one chip router with SpaceWire standard. Thanks to the SpaceWire upper layer protocol (remote memory access protocol: RMAP), the variable length file system operation function can be delegated to the data recorder from the CPU module of the digital electronics of the sensor system. In consequence the infrared spectrometer data from NIRS3 is recorded in parallel with the infrared image sensors. High speed image compression algorithm is also developed for both lossless and lossy image compression in order to eliminate additional hardware resource while maintaining the JPEG2000 equivalent image quality.