Even though Nkunku has scored six goals in seven matches this season, the Frenchman has struggled to secure a permanent spot in Enzo Maresca's starting lineup.
Maresca made 11 changes from the team that beat West Ham 3-0 on Sept 21, but could still start around £400 million (S$680 million) worth of talent.
Joao Felix was another of the Blues’ big money signings to shine. His scooped pass set up Nkunku for opener.
Nkunku then flicked home a second before Felix’s free-kick hit the post and rebounded in off Barrow goalkeeper Paul Farman.
Pedro Neto tapped in Mykhailo Mudryk’s cross for his first Chelsea goal. Nkunku sealed his first hat-trick for the club when he dispossessed Farman and rolled into an empty net.
City began what is likely to be many months without key midfielder Rodri after he suffered suspected knee ligament damage in a fiery 2-2 draw against Arsenal in the Premier League on Sept 22.
Little over 48 hours on from that top-of-the-table clash, City were in action again and Pep Guardiola made nine changes, including a debut for 16-year-old Kaden Braithwaite.
Jeremy Doku, one of the two to retain his place, fired in the opening goal from Jack Grealish’s pass after five minutes.
Rodri’s absence could mean a more prominent role for Matheus Nunes and the Portugal international blasted in his first goal since joining City for £53 million a year ago.
Tom Ince, son of former Manchester United midfielder Paul Ince, pulled a late goal back for Watford, but it was too little, too late for the Championship side.