Carbon estimation hidden in trading is a vital basis for adjusting import/export trading, improving resources use rate and realizing low carbon economy. This paper uses multiple regional input/output to establish a hidden carbon estimation model for bilateral trading from the perspective of industry. It is applied to estimate the net hidden carbon emission between China's bilateral trading with America, Germany, Japan, South Korea, Australia, Russia, India and Brazil by means of WIOD's data from 1997 to 2011, with results showing a net hidden carbon import in bilateral trading between China and America, Germany, Japan and South Korea, a coexisting net carbon import & export between China and Russia, India and Brazil. China generally uses a trading strategy of exchanging carbon emission reduction for trading surplus and exchanging trading deficit for carbon emission reduction. In order to reduce hidden carbon emission, this paper suggests China shall set up carbon emission trading market, consolidate high pollution industries, optimize import/export trading structure and promote imports of high carbon industries and exports of low carbon industries.