The aim of this study was to evaluate the effects of different Se sources on the meat quality and shelf life of fattening pigs. The control diet was supplemented with 0.3 mg/kg of Se from sodium selenite (SS), and experimental diets included 0.3, 0.3 and 0.15 + 0.15 mg/kg of Se from Se-enriched yeast (SY), selenomethionine (Se-Met) and SS + Se-Met, respectively. The results showed that using organic Se or Se + Se-Met in fattening pigs’ diet could increase average daily gain (ADG) (p < 0.05), decrease F/G (p < 0.05), reduce (p < 0.01) moisture, drip loss and cooking loss of longissimus thoracis, as well as increase (p < 0.05) protein and fat contents of longissimus thoracis. Diet supplementation with SY or Se + Se-Met could increase (p < 0.01) back fat thickness and skin thickness, and SY could increase (p < 0.01) belly fat rat. Adding SY or Se + Se-Met could reduce (p < 0.01) L value (45 min, 24 h). Adding Se-Met could decrease (p < 0.01) b value (45 min, 24 h), adding Se + Se-Met could reduce b value (45 min), and adding SY could reduce the b value (24 h). However, there were no (p < 0.05) significant effects on dressing percentage, carcass sloping length, eye muscle area, pH, a value (45 min) and a value (24 h) of longissimus thoracis. Moreover, the TVB-N contents of longissimus thoracis on the first and fifth days, the numbers of Lactobacillus on the third to seventh days and the numbers of E. coli in in the fifth to seventh days of longissimus thoracis were reduced (p < 0.01) by diet supplementation with organic Se. In conclusion, all the results indicate that replacing inorganic Se in diet with organic Se could improve meat quality of fattening pigs. In addition, organic Se could reduce the total volatile basic nitrogen (TVB-N) contents of longissimus thoracis and reduce the numbers of E. coli and Lactobacillus in longissimus thoracis, prolonging the shelf life of pork. These results demonstrated that organic Se supplementation was more effective than SS supplementation for meat quality and the shelf life of fattening pigs.