Stimulated Raman scattering (SRS) microspectroscopy is a powerful imaging technique that leverages chemical composition to produce detailed, label-free images in applications such as biomedical and environmental sciences. However, current SRS methods are often limited by background signals from nonlinear optical phenomena, which reduce contrast and sensitivity. This study introduces a broadband frequency-modulated SRS (FM-SRS) system that enhances flexibility, spectral range, resolution, and automation. Utilizing a high-speed acousto-optic tunable filter and an etalon, the system achieves automated, background-free SRS measurements across the fingerprint to CH-stretch regions. Dynamic selection and adjustment of FM wavenumber pairs maintain high spectral resolution, resolving Raman bands with ∼10 cm−1 linewidths over the 400–3600 cm−1 range. We demonstrate effective background cancellation with phantom specimens and photosynthetic microalgae. This new FM-SRS system addresses the limitations of existing methods, paving the way for advanced applications in SRS microspectroscopy.