The Earth is dramatically carbon poor comparing to the interstellar medium and the proto-sun. The carbon to silicon ratios in inner solar system objects show a correlation with heliocentric distance, which suggests that the destruction of carbon grains has occurred before planet formation. To examine this hypothesis, we perform model calculations using a chemical reaction network under the physical conditions typical of protoplanetary disks. Our results show that, when carbonaceous grains are destroyed and converted into the gas phase and the gas becomes carbon-rich, the abundances of carbon-bearing species such as HCN and carbon-chain molecules, increase dramatically near the midplane, while oxygen-bearing species such as H2O and CO2 are depleted. The carbon to silicon ratios obtained by our model calculations qualitatively reproduce the observed gradient with disk radius, but there are some quantitative discrepancies from the observed values of the solar system objects. We adopted the model of a disk around a Herbig Ae star and performed line radiative transfer calculations to examine the effect of carbon grain destruction through observations with ALMA. The results indicate that HCN, H13 CN and c-C3 H2 may be good tracers of this process.