Benzo(a)pyrene [B(a)P] as a representative polycyclic aromatic hydrocarbons (PAHs) is of worldwide i interest and widely studied in various fields. However, biological and biochemical actions of B(a)P in soil–wheat systems are still rarely reported. In view of the fact that the contents of B[a]P as a ubiquitous soil pollutant in the environment varies greatly, in our study at the laboratory‐scale we explored control factors and aimed to increase basic knowledge of its variations and effects on soil–wheat systems. We studied this for different soil types (red, black, and brown) and for soils newly artificially contaminated (at rates of 0.1, 1, and 10 mg kg−1), to provide some references for complicated 'real' cases. The bioavailability (extractability and bioaccumulation) and basic biological toxicity were tested. Results showed that B(a)P concentrations in soil–wheat (Tritticum aestivum L.) systems extracted by HPCD were insignificantly (p > 0.05) higher than Tenax‐TA, and varied with soil types and spiked concentrations. Also, the root and shoot length were mostly inhibited from 0.88% to 26.35%, and 5.46% to 54.85%, respectively, by B(a)P in different soil types and increased with its increasing concentration. Comparatively, higher bioconcentration factor and translocation factor values were observed under lower group in red soil–wheat systems, and under higher added groups in black and brown soil–wheat systems. Moreover, inhibitive effects posed by B(a)P were mainly targeted at wheat shoots in these soils. This study provided a knowledge of B(a)P in ecosystems with different soil types and specific plant species, further to serve for soil environmental protection with many variations.