Land consolidation engineering is one of the very important ways to improve the quality of farmland and the level of agricultural productivity. Studies of land consolidation and crop cultivation still mainly focus on single land functional optimization or crop breeding and yields. However, whether the improved crop varieties were sown on healthy and fertile soils is still a question. This paper introduces new ideas and engineering measures for sandy land rehabilitation and modern agricultural development in the Mu Us Sandy Land, Shaanxi Province, Western China. The important roles of particles and aggregates in soil reconstruction were confirmed following three innovative microscopic theories, including micro-structure, micro-morphology and micro-mechanism. New soil was constructed based on the physical complementarity of sandy, clay and loess particles in the Yulin area, northern Shaanxi Province. Field experiments were carried out to study the appropriate mixture ratio of different soils and their suitability for different crops. The improved crop varieties were sown on healthy and fertile soils, which were chosen by coupling according to its soil ecological suitability and crop physiological adaptability. The fertility improvement practices in the new constructed soils with different crops integrated water and fertilizer management measures, which were also provided in the experiment. Overall, an integrated land optimization configuration with improved and optimized crop variety selection was suggested for engineering sandy land-oriented consolidation from the soil particles to the agricultural system.