Chinese fir (Cunninghamia lanceolata) is the most important fast-growing coniferous species in China, which is widely used in buildings, furniture and ships. Its heartwood formed earlier, and there are obvious differences between heartwood and sapwood. Rapid detection of chemical composition, cell wall ultrastructure and microstructural differences between heartwood and sapwood of new clones can provide important structural data for evaluating the quality characteristics of heartwood and sapwood. In this paper, the chemical composition of cell wall, crystallinity of cell wall cellulose and microstructure of heartwood and sapwood of Chinese fir clone Yang 61 were determined by Fourier transform infrared spectroscopy, X-ray diffraction, optical microscopy combined with Image J. The results showed that the wave numbers of chemical functional groups in FTIR spectra of heartwood and sapwood were basically the same, that is, the main structure of chemical composition was the same, and the difference between them was mainly in peak intensity. The characteristic peaks of phenols and alcohols (1 034 and 1 122 cm-1) and Caryl-O stretching vibration (1 264 and 1 232 cm-1) in infrared spectra of heartwood were higher than those in sapwood. So this showed that the content of heartwood extracts and the degree of crosslinking of lignin in Chinese fir clones heartwood are possibly higher than those of sapwood. At the same time, the change of relative content of three chemical components was analyzed by characteristic peak ratio method. It was found that the relative content of lignin in heartwood increased by 2%～4%, the relative content of cellulose decreased by 2%, and the hemicellulose content remained unchanged compared with sapwood. By analyzing the X-ray diffraction patterns, it was found that the shape of the diffraction patterns of heartwood and sapwood of Chinese fir were basically the same, but the width of the peak of sapwood was narrower than that of heartwood, and the peak intensity of sapwood was higher at 2θ=22.5°than that of heartwood. The relative crystallinity of heartwood was 35.1% and that of sapwood was 43.1%. There was a significant difference between them at p<0.01. Microscopic images of heartwood and sapwood of Chinese fir were obtained by optical microscopy. The average area and area ratio of tracheid lumen were quickly detected by Image J analysis technology, and it was found that average area and area ratio of tracheid lumen of heartwood were smaller than those of sapwood, that is, heartwood cells have thicker walls and smaller lumens compared with sapwood. The above research found that FTIR, X-ray diffraction, optical microscopy combined with Image J can quickly and accurately detect the differences of microstructure characteristics between wood heartwood and sapwood of Chinese fir clones. The results can provide theoretical guidance and scientific basis for evaluation of physical and mechanical properties, cell wall modification and efficient utilization of heartwood and sapwood.