This study focused on 6-year-old ‘Pawnee’ pecan trees to elucidate the differential responses of physicochemical properties of orchard soil and pecan fruit quality when combining chemical and organic fertilizers. The aim was to unveil the mechanisms that underlie the effects of different fertilization treatments on soil fertility, soil enzyme activities, and pecan fruit quality. Four treatments were established: sole chemical fertilizer (CF; N:P2O5:K2O is 15:15:15), chemical fertilizer combined with cake fertilizer (CF+CC), chemical fertilizer combined with manure fertilizer (CF+M), and chemical fertilizer combined with cake and manure fertilizer (CF+CC+M). Measurements were taken to assess the soil nutrient content, soil enzyme activities, and fruit growth quality in some orchards under different fertilization treatments. The results revealed that the combined application could increase yield and enhance pecan quality. Among these, the CF+M+CC treatment demonstrated the most favorable outcomes, with the pecan kernel oil and unsaturated fatty acid contents reaching 72.33% and 97.54%, respectively. The combined fertilization treatments had no significant impacts on soil trace elements such as Mg, Cu, and Mn; however, it significantly increased the Available Phosphorus (AP), Total Nitrogen (TN), Soil Organic Matter (SOM) and S-ACP (soil acid phosphatase) activities. In summary, the combined application of chemical and organic fertilizers can significantly increase the soil nutrient content and enzyme activities in pecan orchards, to promote the enhancement of fruit quality and economic aspects.