•Minimum data set includes four factors, which reflect the integrated soil function.•Significant differences in soil quality between different productivity.•The significant positive correlation between SQI and wheat yield.•Available N, SOM and microbial biomass N to total N ratio were limiting factors. The double-cropping of winter wheat and summer maize is a major grain production system in China which occupies more than half the double-cropping systems of the country’s dryland area. This cropping system has experienced a decreased crop yield and soil quality and the limiting factors are poorly known. The goal of this study was to conduct a systematic evaluation of wheat yield and soil quality from 132 fields along a regional scale in China. The specific objectives were (i) to establish a minimum data set (MDS) in wheat phase under the wheat-maize cropping system (ii) to evaluate soil quality of the wheat field and determine the factors limiting wheat productivity. The wheat-maize cropping system was partitioned into three productivity levels (high, medium and low) according to the wheat yield. Twenty-six soil indicators, including soil microbiological, chemical and physical factors were measured and analyzed. Using Pearson correlation analysis we identified eight key soil indicators that determine wheat yield. We then used principal component analysis to determine an MDS, which included soil organic matter, alkali-hydrolyzable nitrogen, the ratio of microbial biomass nitrogen to total nitrogen, and available zinc. One-way analysis of variance based on the individual contribution of each MDS indicators under three productivity, revealed available nitrogen, soil organic matter and the ratio of microbial biomass nitrogen to total nitrogen was the most important indicators on limiting wheat yield. A soil quality index (SQI) based on scoring and weighting of MDS indicators was integrated as a tool for assessing farmland soil quality. Based on the MDS, high (HP), medium (MP) and low (LP) productivity received mean SQI of 0.55, 0.48 and 0.39, respectively. The significant positive correlation between SQI and wheat yield suggests that this is a good representative of the MDS for the wheat-maize cropping system in China. We conclude that our SQI may be an effective and practical tool to guide a strategic, regional goal with respect to sustainable high yields.