In multi-branch combs, the comb outputs from the branches suffer from different fiber noises, which often limit the uncertainty of the combs referring a highly-stable optical frequency. To overcome this limitation, we introduced fiber noise difference cancellation to multi-branch fiber combs. We detected and phase-locked the beat notes between the branch outputs and a common 1542 nm continuous wave laser. A piezo-electric transducer-based fiber stretcher was installed in each branch except for the branch used as the cancellation reference. We fabricated two quasi-identical combs with this mechanism and confirmed the relative frequency uncertainty by comparing them. The cancellation improved the frequency uncertainty to a low level of 10-20 at a 100000-s averaging time.