Layered double hydroxide (LDH) nanoparticles (NPs) are safe and effective vectors for small interfering RNA (siRNA) delivery. However, it is unclear whether there are optimal parameters for the efficient delivery of functional siRNA using LDH NPs. In this research, we comprehensively examined the effect of parameters, such as the mixing method and LDH/siRNA mass ratio on siRNA silencing capability. We first noted that the best way for loading gene segments (25 bp dsDNA and siRNA) is to add gene molecules to 100 nm LDH and then diluting in Dulbecco's modified Eagle's medium. Very interestingly, the optimal LDH/gene mass ratio is around 20:1 in terms of cellular uptake amount of gene segments, whereas this ratio is shifted to around 5:1 in terms of target gene silencing efficacy, which has been reasonably explained. The optimization for LDH NP-based gene delivery system may provide the guidance for more efficient in vitro and in vivo siRNA delivery using the optimal parameters.