Single-pixel imaging (SPI) is a computational imaging technique that is able to reconstruct high-resolution images using a single-pixel detector. However, most SPI demonstrations were mainly focused on macroscopic scenes, its application to biological specimens is generally limited by constraints in space-bandwidth-time product and spatial resolution. In this work, we further enhance SPI’s imaging capabilities for biological specimens by developing a high-resolution holographic system based on heterodyne holography. Our SPI system achieves a space-bandwidth-time product of 41,667 pixels per second and a lateral resolution of 4–5 microns, both the two parameters represent the state-of-the-art technical indexes among reported SPI systems. Importantly, our SPI system enables detailed amplitude imaging with high contrast for stained specimens, such as epithelial and esophageal cancer samples, while providing complementary phase imaging for unstained specimens, including molecular diagnostic samples and mouse brain tissue slices, revealing subtle refractive index variations. These results highlight SPI’s versatility and establish its potential as a powerful tool for advanced biomedical imaging applications.