Earth-abundant molybdenum disulfide (MoS₂), as a promising substrate for surface-enhanced Raman spectroscopy (SERS), has attracted considerable attention. Naturally occurring MoS₂ primarily exists in the semiconducting 2H phase, but its SERS performance is limited because active sites are typically confined to its edges. Furthermore, the irregular agglomeration of MoS₂ can lead to performance degradation, making natural semiconducting material unsuitable for practical applications. Therefore, enhancing the performance of MoS₂ in the field of SERS is of great significance. Metal-organic frameworks (MOFs) are ideal materials for building efficient SERS substrates due to their tunable pore structures. Among various MOF materials, zeolitic imidazolate frameworks (ZIFs) have aroused significant interest due to their well-defined polyhedral structures, homogeneity, and small particle sizes. Therefore, in this study, MoS₂/zeolitic imidazolate framework-67 (ZIF-67) heterostructures are prepared by the hydrothermal method as SERS substrates, which exhibits exceptionaly high sensitivity to rhodamine 6G with an enhancement factor of up to 6.68×10⁶. Moreover, after SERS is exposed to air for four months, its performance remains almost unchanged, demonstrating high stability and reusability. To evaluate the actual detection ability of this substrate, bilirubin is selected as the analyte, which is a clinically relevant metabolic waste. Since both high and low concentrations of free bilirubin can lead to cardiovascular and cerebrovascular diseases, accurate monitoring of bilirubin levels is crucial for diagnosing bilirubin-induced disorders. Using the MoS₂/ZIF-67 substrate, the label-free detection of bilirubin is achieved with a limit of detection as low as 10^–10 mol/L. The outstanding performance of this substrate can be attributed to the vertically aligned MoS₂ nanostructure, which exposes more active sites. Additionally, ZIF-67 provides a high specific surface area and abundant porous structures, providing numerous adsorption sites for target molecules. Furthermore, the internal charge transfer facilitates the formation of a highly conductive 1T phase, thereby improving electrical conductivity. This work provides valuable insights into the rational designing of noble-metal-free materials for highly sensitive SERS detection.