Pendimethalin has been considered a moderately to extremely toxic compound for fish and aquatic organism. This study developed the determination of dynamic residual distribution for pendimethalin in crucian carp tissues (muscle, liver, kidney, gill, and blood) under semistatic exposure system by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method. The pendimethalin residues in various fish tissues increased initially and then decreased, and the residue amount of pendimethalin varied from tissue to tissue of crucian carp. Particularly, the pendimethalin accumulation in most fish tissues made significant decreases at two-time points. Pendimethalin was initially absorbed and enriched by fish body, and then partial pendimethalin was discharged into the outside environment through the metabolism function of crucian carp. The residue levels of pendimethalin distributed in crucian carp were ranked in the following decreasing order: liver > kidney > gill or muscle > blood, attributed to the fact that pendimethalin tends to accumulate in lipid-rich tissues of fish. Risk assessment results indicated that the chronic risk from dietary exposure to pendimethalin through crucian carp consumption for Chinese residents was acceptable, along with a lower estimated exposure dose (EED) than acceptable daily intake (ADI) and risk quotient (RQ) < 1. This study performed the first analysis for pendimethalin residual distribution in crucian carp tissues under semistatic exposure condition and provided a reference for pollution control and risk assessment of pendimethalin aimed at aquatic products.