Synchrotron-based soft X-ray micro analysis is a powerful technique for the quantitative molecular characterization of submicron-sized organic samples without damage. Recent development of X-ray Absorption Near Edge Structure (XANES) spectroscopy using Scanning Transmission X-ray Microscope (STXM) has enabled the comprehensive study on the chemical history of the early solar system as recorded in organic molecules ranging from the most primitive to altered extraterrestrial materials. In this review paper we describe our two achievements: one is the results of STXM μ-XANES analyses performed on organic-containing particles extracted from 81P/Wild 2 cometary dust tracks collected by the Stardust comet sample return mission. The XANES spectra have revealed highly complex organic structures with a large heterogeneity in heteroatom content and different functional groups, suggesting that the comet organics may have multiple precursors. Another result is the molecular spectroscopic data on meteoritic organic matter spanning various chondrite classes, groups, and petrologic types, using carbon XANES spectroscopy. The sample analyses and the kinetics through heating experiment have shown that the intensity of 1s→σ* exciton derived from highly conjugated sp² carbon in the type 3+ chondritic organic matter appears to quantitatively determine the parent body metamorphism.