Femtosecond laser two-photon polymerization (TPP) technology, known for its high precision and its ability to fabricate arbitrary 3D structures, has been widely applied in the production of various micro/nano optical devices, achieving significant advancements, particularly in the field of photonic wire bonding (PWB) for optical interconnects. Currently, research on optimizing both the optical loss and production reliability of polymeric photonic wires is still in its early stages. One of the key challenges is that inadequate metrology methods cannot meet the demand for multiphysical measurements in practical scenarios. This study utilizes novel in situ scanning electron microscopy (SEM) to monitor the working PWBs fabricated by TPP technology at the microscale. Optical and mechanical measurements are made simultaneously to evaluate the production qualities and to study the multiphysical coupling effects of PWBs. The results reveal that photonic wires with larger local curvature radii are more prone to plastic failure, while those with smaller local curvature radii recover elastically. Furthermore, larger cross-sectional dimensions contribute dominantly to the improved mechanical robustness. The optical-loss deterioration of the elastically deformed photonic wire is only temporary, and can be fully recovered when the load is removed. After further optimization based on the results of multiphysical metrology, the PWBs fabricated in this work achieve a minimum insertion loss of 0.6 dB. In this study, the multiphysical analysis of PWBs carried out by in situ SEM metrology offers a novel perspective for optimizing the design and performance of microscale polymeric waveguides, which could potentially promote the mass production reliability of TPP technology in the field of chip-level optical interconnection.