Geometric deviation associated with the assembly of sheet metal is a general concern for manufacturers. The typical assembly step involves a sequence of events that exert forces on the parts to enforce them to the nominal condition and to connect the parts together. The simulation and optimization of the assembly steps often neglect the sequence of operations due to the problem and computation complexity. This paper investigates the influence of the clamping sequence in the body-in-white (BIW) manufacturing process on the geometrical quality of the assembly. An approach for modeling clamping sequences for non-rigid variation simulation is introduced in a digital twin context, taking the part deviation into consideration. An optimization method is proposed to achieve minimum geometric deviation after clamping the parts and welding them together. The method is successfully applied on two reference assemblies, and the results show that the sequence of clamping can impact the total geometric deviation up to 31%. Combining clamping and welding sequence optimization can enhance the quality improvement to 77% after releasing the assembly from the fixture and springback.