The variational assimilation theory is generally based on unbiased observations. In practice, however, almost all observations suffer from biases arising from observational instruments, radiative transfer operator, precondition of data, and so on. Therefore, a bias correction scheme is indispensable. The current scheme for radiance bias correction in the GRAPES 3DVar system is an offline scheme. It is actually a static correction for the radiance bias before the process of cost function minimization. In consideration of its effects on forecast results, this kind of scheme has some shortcomings. Thus, this study provides a variational bias correction (VarBC) scheme for the GRAPES 3DVar system following Dee’s idea. In the VarBC scheme, the observation operator is modified and a new control variable is defined by taking the predictor coefficients as the control parameters. According to the feature of the GRAPES-3DVAR, an incremental formulation is applied and the original bias correction scheme is maintained in the actual process of observations. The VarBC is designed to co-exist with the original scheme, because it is a dynamic revision to the observational operator on the basis of the old method, i.e., it adjusts the model state vector along with the control parameters to an unbiased state in the process of minimization and the assimilation system remains consistent with available information automatically. Preliminary experimental results show that the mean departures of background-minus-observation and analysis-minus-observation are reduced as expected. In a case study of the heavy rainfall that happened in South China on 11–13 June 2008, the 500-hPa geopotential height is better simulated using the analyzed field from the VarBC as the initial condition.