Terrestrial laser scanning (TLS) is a promising technology for quantity checking huge grain stocks with low cost, light workload and high efficiency. Existing applications of TLS in bulk grain measurement and quantification lack the ability to capture complete structural information of grain bulks and thus will result in large errors. In this paper, we propose a bi-temporal TLS scheme for fast 3D modeling and accurate volume measurement of bulk grains stored in large warehouses. The scheme uses bi-temporal multi-site TLS datasets acquired under both empty and full or high loading conditions to obtain complete surface information about grain bulk’s structure. In order for a grain bulk’s all external surfaces and the 3D volumetric model reconstructed therefrom to be automatically derived from the bi-temporal TLS dataset, several dedicated methods are developed for the scheme. A fully automated marker-free strategy exploring structurally semantic information inherent in the large grain storehouses is adopted to register multi-scan TLS point cloud data captured in large-scale granary scenes. Also, a local minima-based region growing technique is devised to extract underlying surfaces from a granary scene point cloud model. Experiments show that the proposed 3D modeling and volume measurement scheme can work effectively and quickly in TLS-based granary field applications and repeated test data demonstrate its correctness, repeatability and accuracy. Compared with the conventional manual measurement approach, the bi-temporal TLS scheme can not only achieve much higher measurement precision, but also greatly improve efficiency by significantly reducing cost, workload, and manpower. It has good potential for use in the area of nation-wide grain inventory inspection in China.