Near-infrared (NIR) photodetectors (PDs) have attracted much attention in noninvasive medical diagnosis and treatment. Especially, the self-filtered NIR PDs are highly demandable for tremendous biomedical application due to their strong ability in wavelength discrimination. In this work, we designed and then fabricated a Si micro-holes array/Graphene (Si MHA/Gr) van der Waals (vdW) Schottky NIR photodiode by using PbS quantum dots (QDs) coating. The device exhibits a unique self-filtered NIR response with a responsivity of 0.7 A/W at -1 V and a response time of 61 μs, which are higher than that without PbS QDs coating and even most of previous Si/Gr Schottky photodiodes. The light trapping of the Si MHA and the PbS QDs coating can be attributed to the high responsivity of the vdW photodiode. Furthermore, the presented NIR photodiode can also be integrated in photoplethysmography (PPG) for real-time heart-rate (HR) monitoring. The extracted HR is in great accord with the value measured with the patient monitor by analyzing the Fourier transform of the stable and reliable fingertip PPG waveform, suggesting its potential for practical applications.