Functional nucleic acids (FNAs) are promising sensing elements, and extensive interests are excited to integrate FNAs with transducers for biochemical assays. However, efforts for FNAs modified light-addressable-potentiometric-sensor (FNA-LAPS) are rarely reported. LAPS is a versatile transducer with electrolyte-insulator-semiconductor (EIS) structure and can respond almost to any surface electronic deviation. Herein, organized studies for FNA-LAPS including experiments, theoretical derivations, and MEDICI (Synopsys) simulations are presented using Pb2+-DNAzyme GR-5 and Ag+-aptamer as proof-of-concepts, which are typical FNAs with distinctive sensing strategies. First, the on-LAPS occurrences of FNAs and their particular sensing actions are evidenced by tracking their X-ray photoelectron spectroscopy (XPS) core spectra of N 1s, P 2p, C 1s, Ag, etc. Then, applications of FNA-LAPS are executed by a homemade and mobile-phone controlled system, the limit-of-detection is 0.01 ppb, sensitivities are 2.86 (Pb2+) and 1.53 (Ag+) mV/log10(ppb) ( R2 = 0.98), respectively. Furthermore, a charge and resistor mechanism (C&R) is proposed to illustrate the measured LAPS responding for FNAs and their sensing behaviors (Pb2+-mediated cleavage and Ag+-mediated folding), based on carefully analyzing basic LAPS' experimental data and MEDICI calculated distributions of build-in potentials, energy-bands, carriers, etc., at the EIS microinterface (semiconductor side). Finally, demonstrations for C&R based FNA-LAPS principle are provided by the use of MEDICI, as a means to bridge experiments and theoretical deductions. In general, a cross-study for FNA-LAPS is proposed including XPS characterization, biochemistry detection, theoretical analysis, and MEDICI simulation, it is believed their powerful combination would provide an ideal workstation for analytical chemistry applications, not only the traditional determinations but also facilitations for investigating FNAs' configurational transformations.