The asteroid 3904 Honda is named after him, 8485 Satoru is named after his wife, and 11442 Seijin-Sanso is named after his astronomical observatory.
Asteroid 3904 Honda je pojmenován po Hondovi, 8485 Satoru je pojmenován po jeho ženě, a 11442 Seijin-Sanso je pojmenován po astronomické observatoři na níž působil.