Ion channels in cell membranes are gated, water-filled pores that allow passive transport of ions across the membrane along their electrochemical gradient. Recent studies have shown that nanoparticles can interact with ion channels and change their currents kinetics properties of the channel. In this study, we used the transient receptor potential (TRP) channel currents in retinal pigment epithelial (RPE) cells recorded by whole-cell patch clamp technique to observe the silica nanoparticle-ion channel interaction. For whole cell recordings, we clamped membrane potential to −40 mV and used a ramp of 1000 ms duration for stimulation. The ramp was increased from −140 mV to +60 mV. We used windowed scalogram entropy and compared the results with windowed scale index method. Our results indicated that the temporal change of entropy using windowed scalogram entropy method is sensitive to demonstrating the effect of silica nanoparticles on RPE cell TRP currents. Furthermore, windowed scale index can analyze the temporal fluctuations in the aperiodicity of cell membrane current signals. Our findings suggest that entropy measurement methods may be useful in the function analysis of cell ion channels.