Surface‐enhanced Raman scattering (SERS) substrate is the key to SERS technology and it is still a basic focus to fabricate desirable SERS substrates offering multiple advantages of strong Raman enhancement and good reproducibility and portability. A flexible paper‐based SERS substrate were fabricated involving the use of Au nanocubes (NCs) monolayer. Au NCs were generated with tunable size in the range of 24 to 63 nm through seed‐mediated growth method. The effect of support on SERS properties of Au NCs–assembled monolayer was systemically explored. As a result, more excellent SERS performance could be obtained by assembling Au NCs on the filter paper. Besides, the influence of Au NCs' size on SERS‐enhanced effect of paper‐based substrate was also investigated. Our results clearly indicated that paper‐based substrate with 39 nm Au NCs possessed the optimal SERS enhancement. This SERS substrate exhibited high sensitivity with enhancement factor (EF) up to 9.75 × 107 and demonstrated good uniformity and time stability. Furthermore, based on this superior paper‐based SERS substrate with advantage of powerful sample extraction performance, the measurement of crystal violet (CV) on shell surface were successfully carried out with detection limit down to 2.17 × 10−7 M. And linear quantification were achieved in the range from 5 × 10−5 to 5 × 10−7 M. To sum up, the as‐prepared SERS substrate is applicable for on‐site detection and analysis of CV on various shell surfaces.