The nanoparticle density (PD) of the substrates is crucial for surface‐enhanced Raman scattering (SERS) performance. Here, bottom‐up SERS substrates based on rough gold nanorods (R‐Au NRs) with different PD are fabricated and their SERS property are investigated. In particular, R‐Au NRs are deposited on the Si wafer from sparse to dense through electrostatic interaction and from monolayer to multiple layers by interface self‐assembly technique. It is found that the SERS intensity increases dramatically with increasing PD and remains almost unchanged when the PD increases to 241.22 counts µm−2, and the limited penetration depth of laser is the reason for the intensity saturation. Additionally, similar results are observed in the smooth Au NRs substrates, re‐confirming the PD‐dependent SERS performance. Importantly, the SERS activity of R‐Au NRs substrates is higher than smooth Au NRs substrates in each PD, indicating that R‐Au NRs can produce stronger electromagnetic field enhancement, which is supported by the theoretical simulation results. Finally, it is demonstrated that the optimal SERS substrates can be effectively utilized for the quantitative measurement of thiram in soil. Briefly, the PD of substrates has a great impact on SERS activity, which offers an idea for the design of highly efficient SERS substrates.