Aiming at the problem of difficulty in updating the algorithm software of embedded atmospheric sensing system, a data solving card is designed, which can update program in application.With DSP+FPGA structure as the core, the data solving card ensures the I2C transmission process is not interrupted by use of special interrupt control logic. The sector structure of Flash is used for reliable implementation of in-application programming. The simulation results show that the data solving card can realize the in-application programming of the calculating software in a simple and quick way, and meet the running requirements of common embedded sensor system algorithm software.