This paper studies the fuel supply offset of diesel engines based on the crankshaft segment signal. Engine nonuniformity refers to the crankshaft torque fluctuation caused by cylinder-to-cylinder differences caused by misfiring or differences in the fuel supply or air supply. Fuel injection offset can reduce the nonuniformity between cylinders to realize high-efficiency and low pollution combustion. Based on crankshaft segment signal characteristics, an individual cylinder fuel offset control (FOC) strategy was built. The high-pressure common-rail diesel engine operating nonuniform control strategy was put forward. Based on crankshaft segment signal characteristics at different operating conditions, the reasonable operating condition of detecting the engine individual cylinder nonuniform degree was put forward. The open-loop and closed-loop control mode based on the condition was set up. The proportional-integral (PI) control algorithm is proposed to quantify engine individual cylinder nonuniform degree, and the fuel amount offset value was obtained. According to the principle of FOC, based on the automotive electronics development ASCET software platform, the FOC strategy module of the electronic control unit (ECU) was designed, and the simulation experiment was carried out. Research shows that for Z cylinder engine, just the first Z/2 harmonic components below fire frequency can fully reflect the state of the engine’s nonuniform operation. The control target to individual cylinder FOC is zero for the synthetic waveform amplitude of the first Z/2 harmonic components. Compared with the traditional quantization method, the fuel offset information extracted from the crankshaft segment signal has stronger anti-interference and more accurate parameters. FOC algorithm can accurately reflect the engine’s operating nonuniformity. The control of the nonuniformity is reasonable. The offset fuel amount calculated by FOC is very consistent with the fuel supply state of each cylinder set by the experiment, which meets the requirement of accurate fuel injection control of the diesel engine.