A randomized block field experiment was conducted in the irrigated area of northern Xinjiang, China, to clarify the effects of biochar (0, 30 × 103 kg·hm−2 (B)) combined with nitrogen (0, 150 (N1), and 300 kg·hm−2 (N2)) on soil fertility, which was represented by CK, B, N1, N2, BN1, and BN2, respectively. The performance of eleven indices related to soil chemical, physical, and biological properties was evaluated by factor analysis and cluster analysis to determine the most appropriate mode for soil fertilization and to identify the main soil environmental factors affecting wheat yield under biochar combined with nitrogen. The results indicated that the first factor was the activity factor, including the Shannon index, McIntosh index, and Simpson index. The second factor was the available nutrient factor, including organic matter, available phosphorus, and available potassium. Factor 3 can be taken as the nutrient-supplying and retaining factor containing total phosphorus, total potassium, and bacterial quantity. The highest score of soil quality was observed in the BN1 treatment, followed by the BN2 and B treatments, which were almost in line with the results of wheat yields. Cluster analysis classified six treatments into four main groups on the basis of the measured parameters, which was mostly consistent with the results of soil quality scores. Considering both economic and environmental benefits, 30 × 103 kg·hm−2 biochar combined with 150 kg·hm−2 nitrogen was the best combination to restore crop productivity and soil quality and to achieve nitrogen decrease and benefit increase. This study provided the scientific basis for the rational fertilization and scientific management of biochar combined with nitrogen fertilizer in the irrigated area of northern Xinjiang, China.