The thermoelectric generator (TEG) technology is important for improving energy efficiency. However, the TEG limited by poor thermoelectric material properties and thermal transfer strategies faces challenges in achieving excellent heat harvesting capacity, especially for large-temperature gradients. Herein, we reported a heat pipe-enhanced two-stage thermoelectric generator (HTTEG) enabled by bismuth alloy-based PCM for effective space waste thermal harvesting. We comprehensively explored the effects of different thermal-enhanced strategies on HTTEG performance. Compared with copper plate and horizontal layout, the effective thermal conductivity obtained by vertical-planar heat pipe is 1.1 × 104 W/mK enhanced by 79.2 and 33.0 times, which has outstanding advantages in achieving considerable temperature difference and excellent thermoelectric harvesting capacity of the HTTEG. We also systematically discussed the thermoelectric properties of heat pipe-enhanced one-stage TEG (HOTEG) and HTTEG by simulation and LED test bench. The results show that the bismuth alloy-based PCM with considerable latent thermal capacity and remarkable heat transfer characteristics can suppress temperature fluctuations and expand thermoelectric harvest interval, achieving excellent power output capacity. Compared with the HOTEG, the thermoelectric power achieved by HTTEG is 4.45 W enhanced by 581.8 %, because optimizing the spatial layout of stage-two thermoelectric modules to the high-temperature gradient interval achieves remarkable heat harvesting efficiency.