We investigate anomalous strong lens systems, particularly the effects of weak lensing by structures in the line of sight, in models with long-lived electrically charged massive particles (CHAMPs). In such models, matter density perturbations are suppressed through the acoustic damping and the flux ratio of lens systems are impacted, from which we can constrain the nature of CHAMPs. For this purpose, first we perform $N$-body simulations and develop a fitting formula to obtain non-linear matter power spectra in models where cold neutral dark matter and CHAMPs coexist in the early Universe. By using the observed anomalous quadruple lens samples, we obtained the constraints on the lifetime ($tau_{rm Ch}$) and the mass density fraction ($r_{rm Ch}$) of CHAMPs. We show that, for $r_{rm Ch}=1$, the lifetime is bounded as $tau_{rm Ch} < 0.96,$yr (95% confidence level), while a longer lifetime $tau_{rm Ch} = 10,$yr is allowed when $r_{rm Ch} < 0.5$ at the 95% confidence level. Implications of our result for particle physics models are also discussed.