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We report on the experimental study of flip chip bonded niobium-based superconducting multichip module (MCM) using a nano-engineered cryogenic adhesive (nECA) for a cryogenic underfill that uses single-wall carbon nanotubes. Two MCMs, each having a 5 × 5 mm2 chip flip chip bonded onto a 1 × 1 cm2 carrier chip, were made with the nECA and pure cryogenic underfill for comparative analysis. The MCMs (1 × 2) were then mounted on a cryocooler and the thermal performances of the two modules were compared. The MCM bonded using nECA demonstrated a 58% decrease in temperature gradient between chip and carrier with respect to the pure cryogenic underfill. Additionally, we report the I-V characteristic of 20 unshunted Josephson junctions on the chip and the carrier as a function of carrier temperature and applied power for the MCM bonded using nECA. The MCM was thermal cycled between room temperature and 4.2 K, and the I-V measurements were repeated at 4.2 K. The experimental study demonstrated that single-wall carbon nanotubes integrated underfill enhanced the thermal performance without affecting the electrical performance. This finding presents a novel nano-engineered packaging material and approach for increased functional modularity for superconducting MCMs.