Long-term vegetable production in plastic shed soil (PSS) and related soil management strategies stimulate the changes of soil properties and the mobilization of selenium (Se), causing risks to environmental soil quality and human health. Nevertheless, whether the greenhouse management (defined by the years of greenhouse vegetable production) and the greenhouse type have a synergistic effect on Se mobility in PSSs subjected to long-term vegetable production is still unclear. This study investigated the joint effects of greenhouse management and the properties of PSS on Se adsorption and desorption in soils collected from solar greenhouses (SG) and round arch plastic greenhouses (PG), which has been continuously cultivated respectively for 20 and 30 years in Tongshan County, Jiangsu Province, East China. Herein, we carried out a field survey coupled with batch experiments to investigate the adsorption and desorption behavior of Se in the SG and PG soils with different years of vegetable production. Results showed that greenhouse management had differentiated effects on soil properties and Se mobility in the two typical PSSs. Compared to the open field soils, long-term vegetable production generally increased soil nutrients (i.e., total P (TP), available P (AvP)), OM and Se desorption in the SG soil, while it significantly decreased Se adsorption in both typical PSSs. The soil pH had a downward trend with the increase of the years of vegetable production. The longer years of greenhouse vegetable production, the less Se adsorption capacity occurred in PSSs with annual decrease rates of 0.48 and 0.24 mg kg−1 yr−1 for the SG and PG soil, respectively, at 1.0 mg L−1 Se addition. Conversely, the ratio of Se desorption of the SG soils increased with longer vegetable production. The results of partial least squares regression (PLSR) explained the differences in Se adsorption and desorption between the SG and PG soil due to the changes in soil properties caused by the greenhouse management and greenhouse type. The fewer Se application is therefore recommended in the SG soils than in the PG soils after long-term greenhouse vegetable production.