Flexible thermoelectric (TE) materials have attracted increasing interest due to their potential applications in energy harvesting and high-spatial-resolution thermal management. However, a high-performance flexible micro-TE device (TED) compatible with the modern electronics fabrication process has not yet been developed. Here we report a general van der Waals epitaxial growth approach to fabricating a freestanding and flexible hybrid comprised of single-wall carbon nanotubes and highly ordered (Bi,Sb)2Te3 nanocrystals. High power factors ranging from ~1,680 to ~1,020 µW m−1 K−2 in the temperature range of 300-480 K, combined with a strongly depressed thermal conductivity yield an average figure of merit of ~0.81. A prototype flexible micro-TED module consisting of two p-n hybrids was then fabricated, which demonstrated an unprecedented open circuit voltage of ~22.7 mV and a power density of ~0.36 W cm−2 under a ~30 K temperature difference, and a net cooling temperature of ~22.4 K and a heat absorption density of ~92.5 W cm−2.