This study was designed to investigate the effect on wheat yield of applying organic fertilizers (OF) with five different selenium (Se) concentrations. The mineral nutrients, cadmium (Cd) content, and the distribution of Se in wheat plants were also measured. The results showed that wheat yields reached a maximum of 9979.78 kg ha in Mengcheng (MC) County and 8868.97 kg ha in Dingyuan (DY) County, Anhui Province, China when the application amount of selenium-containing organic fertilizer (SOF) was up to 600 kg ha. Among the six mineral nutrients measured, only the calcium (Ca) content of the grains significantly increased with an increase in the application amount of SOF in the two regions under study. Cd content showed antagonistic effects with the Se content of wheat grains, and when the SOF was applied at 1200 kg ha, the Cd content of the grains was significantly reduced by 30.1% in MC and 67.3% in DY, compared with under the Se0 treatment. After application of SOF, the Se content of different parts of the wheat plant ranked root > grain > spike-stalk > glume > leaf > stem. In summary, SOF application at a suitable concentration could increase wheat yields and significantly promote the Ca content of the grains. Meanwhile, the addition of Se effectively inhibited the level of toxic Cd in the wheat grains.