This study compared the body composition and strength of the lower extremity parameters between novice runners (NRs) and amateur marathon runners (AMRs). A total of 50 NRs (33.84 ± 4.32 years) and 50 AMRs (33.36 ± 5.55 years) were analyzed cross-sectionally. Bioelectrical impedance analysis measured body composition parameters, and isokinetic testing assessed knee muscle strength. The results showed that compared to AMRs, NRs had lower fat-free mass (FFM), skeletal muscle mass (SMM), and total body water (TBW) (−15, −12, and −5%; all p < 0.01) but higher body fat percentage (PBF) and visceral fat area (VFA) (+27 and +32%; both p < 0.01). They also had 6% lower knee extensor (KE) strength and 31% lower knee flexor (KF) strength on the dominant legs (DLs) and 14% lower KF strength on the non-dominant legs (NDLs). In addition, their hamstring–quadriceps ratio (H: Q) was 24% lower on the DLs and 9% lower on the NDLs. The NRs exhibited significant negative correlations between PBF, VFA, and knee muscle strength (r = −0.54 to −0.42, p < 0.01), while the AMRs had significant negative correlations only for PBF (r = −0.59 to −0.57, p < 0.001). In conclusion, the NRs exhibited lower FFM and TBW, higher PBF and VFA, and reduced muscle strength. In contrast, the AMRs exhibited the opposite pattern. These findings suggest that NRs with elevated body fat (BF) indicators should prioritize fat reduction and performance enhancement, while those with lower muscle mass require targeted programs to increase muscle capacity and joint stability. This approach may advance them toward the level of AMRs. Future studies should adopt longitudinal designs to explore how training interventions influence the physiological adaptations observed in runners at different experience levels.