Strongly correlated materials feature technologically relevant functionalities such as high-temperature superconductivity and colossal magnetoresistance, which emerges from the competition and coexistence of electronic and magnetic phases. Uncovering the microscopic interactions underlying these phenomena remains challenging because spin, orbital, charge, and lattice degrees of freedom are inherently intertwined. Here, by combining time-resolved X-ray diffraction and polarization-resolved ultrafast optical reflectivity in La1/4Pr3/8Ca3/8MnO3, we reveal that coherent phonon modes can selectively track different ordered phases: the in-plane phonon response is predominantly sensitive to charge/orbital order, and the c-axis phonon response is sensitive to magnetic order. Moreover, a ferromagnetic-related hysteresis emerges even when solely probing the charge/orbital-ordered phase, indicating a strong microscopic coupling between the spatially separated charge/orbital-ordered and ferromagnetic-ordered phases. These results demonstrate that coherent phonons provide a direct time-domain route to disentangle intertwined electronic and magnetic dynamics in coupled phases.