Formation of bound residues (BR) has generally been considered as a detoxification process for organic contaminants. BR is an indispensable component for risk assessment of pesticides. In this study, BR of 14C-pyraoxystrobin in three soils cultivated for 100 days were characterized in light fraction (LF), loosely combined humus (LCH), stably combined humus (SCH), humic acid (HA), fulvic acid (FA), and humin. Isotope labeling technique was used to detect the distribution of BR of 14C-pyraoxystrobin in the six fractions of soil organic matter (SOM). The results showed that the amount of total BR was positively correlated with the SOM content (p < 0.05). The BR of 14C-pyraoxystrobin in cambisol soil was largest at 31.26 ± 0.04% of the induced radioactivity. During the whole incubation period, the BR of pyraoxystrobin in LCH of the three soils were consistently higher than that in SCH, and the amount of BR in FA was consistently greater than that in HA. The BR of 14C-pyraoxystrobin bound with humin increased over time. In addition, a degradation product 3-(4-chlorophenyl)-1-methyl-1H-pyrazol-5-ol (M1) from the hydrolysis of pyraoxystrobin was detected in cambisol soil, indicating the bonding of M1 with the HA separated from LCH (HALCH) via ester or ether linkages. The results provide new insights into the fate of BR of pyraoxystrobin in soils and may help to develop an understanding for the risk assessment of pyraoxystrobin and other strobilurin fungicides.