The factor analysis of water resources and energy security in Shenzhen in 1996–2015 was carried out. Economic and average factor (f₁), population and elasticity factor (f₂) are two main factors. f₁ shows the threat of supporting the city’s normal operation to water resources and energy security, with a weight of 68%. f₂ shows the uncertainty brought about by the increments of economic and population to water energy system safety, with a weight of 32%. The composite score shows that the total water energy system safety in Shenzhen tends to decline. This conclusion accords with the actual situation of water energy system in Shenzhen municipality. It shows that the evaluation model is effective for the analysis of water energy security situation in Shenzhen, and can provide reference for the decision-making of Shenzhen municipality.