To improve the SpO$_2$ sensing system performance for hypoperfusion (low perfusion index) applications, this paper proposes a low-noise light-to-frequency converter scheme from two aspects. First, a low-noise photocurrent buffer is proposed by reducing the amplifier noise floor with a transconductance-boost ($g_{m}$-boost) circuit structure. Second, a digital processing unit of pulse-frequency-duty-cycle modulation is proposed to minimize the quantization noise in the following timer by limiting the maximum output frequency. The proposed light-to-frequency sensor chip is designed and fabricated with a 0.35-$\mu$m CMOS process. The overall chip area is 1 × 0.9 mm$^2$ and the typical total current consumption is about 1.8 mA from a 3.3-V power supply at room temperature. The measurement results prove the proposed functionality of output pulse duty cycle modulation, while the SNR of a typical 10-kHz output frequency is 59 dB with about 9-dB improvement when compared with the previous design. Among them, 2–3 dB SNR improvement stems from the gm-boosting and the rest comes from the layout design. In-system experimental results show that the minimum measurable PI using the proposed blood SpO$_2$ sensor could be as low as 0.06% with 2-percentage-point error of SpO$_2$. The proposed chip is suitable for portable low-power high-performance blood oximeter devices especially for hypoperfusion applications.