Ground Penetrating Radar (GPR) is a widely-utilized non-destructive detection tool. Full Waveform Inversion (FWI) offers a reliable algorithm for accurately imaging GPR data. Despite its potential, FWI's effectiveness is often compromised by unknown excitation sources, which can lead to computational failures and/or diminished imaging accuracy. Addressing this challenge, this paper introduces a convolution-type objective function designed to mitigate the detrimental effects of these unknown excitation sources on FWI imaging. Critical to the success of this function is the precise selection of reference traces. Further refining the capability for signal separation, we have integrated Squeeze-and-Excitation (SE) modules into the traditional Wave-U-Net architecture, culminating in the development of the SE-Wave-U-Net framework. This framework is adept at dynamically extracting accurate reference traces from field GPR data, which are essential for the accurate FWI imaging. The efficacy, accuracy, and practical applicability of proposed methods are validated through extensive analysis of numerical, laboratory experiments, and field GPR data. The proposed algorithm not only establishes a high-precision computational framework for FWI but also enhances the reliability of GPR imaging in complex environments.