This empirical study compares the effects of face-to-face and online communication in driving innovation output at the regional level under the traffic constraints imposed by the COVID-19 pandemic, to examine whether innovation can overcome spatial barriers through online communication. We first developed an empirical model that attributes co-patent innovation output growth to physical communication, online communication, and other related factors. Our findings indicate that online communication can partially substitute offline interactions, though not as effectively. The analysis of spatial changes in innovation during the pandemic reveals two main evolutions: localization and polarization. These shifts in innovation behavior are primarily driven by communication dynamics, highlighting the proximity of face-to-face communication and the concentration of online communication interactions. Our results suggest that innovation clusters and networks will persist in shaping spatial patterns of innovation. This study offers important insights for enterprises, emphasizing the ongoing role of face-to-face communication in fostering innovation. It also provides a new explanation for the lower effectiveness of videoconferencing compared to F2F interactions, particularly in real-world settings beyond controlled experiments.