We propose a scheme for near-field thermophotovoltaic (TPV) energy conversion, where thermal emission from an emitter is extracted by an intermediate transparent substrate attached to the top of a photovoltaic (PV) cell. The addition of an intermediate transparent substrate suppresses the unwanted heat transfer from the emitter to the PV cell due to the surface modes on the PV cell while maintaining the enhancement in the interband absorption. We confirm that our scheme is applicable for near-field TPV systems using a silicon (Si) or tungsten (W) emitter. As a specific example, we designed a near-field TPV system composed of a one-dimensional Si photonic crystal thermal emitter, an InGaAs PV cell, and an intermediate Si substrate, and displayed that our scheme could realize both high power density (>5 × 104 W/m2) and high power conversion efficiency (>40%) at a 50-nm gap between the emitter and the intermediate substrate.