With the development of technology and methodologies, Raman spectrometers are becoming efficient candidate payloads for planetary materials characterizations in deep space exploration missions. The National Aeronautics and Space Administration (NASA) already deployed two Raman instruments, Super Cam and SHERLOC, onboard the Perseverance Rover in the Mars 2020 mission. In the ground test, the SHERLOC team found an axial offset (~720 μm) between the ACI (Autofocus Context Imager) and the spectrometer focus, which would obviously affect the acquired Raman intensity if not corrected. To eliminate this error and, more importantly, simplify the application of Raman instruments in deep space exploration missions, we propose an automatic focusing method wherein Raman signals are optimized during spectrum collection. We put forward a novel method that is realized by evaluating focus conditions numerically and searching for the extremum point as the final focal point. To verify the effectiveness of this method, we developed an Auto-focus Raman Probe (SDU-ARP) in our laboratory. This method provides a research direction for scenarios in which spectrometers cannot focus on a target using any other criterion. The utilization of this auto-focusing method can offer better spectra and fewer acquisitions in focusing procedure, and the spectrometer payload can be deployed in light-weight bodies (e.g., asteroids) or in poor illumination conditions (e.g., the permanently shadowed region in the Lunar south polar area) in deep space exploration missions.