This paper examines the importance of spatial proximity in research collaborations, focusing on China’s transportation infrastructure advancements. Analyzing academic papers published by Chinese institutions over three decades, we find that collaboration probability is positively correlated with institutions’ research output and negatively correlated with geographic distance. When considering other dimensions of proximity, administrative proximity and social network proximity exhibit the most substantial influence. Employing staggered difference-in-differences methods, we then establish causal inferences by investigating the effects of direct flight routes and high-speed rail (HSR) connections. Findings show that both modes of transportation contribute to enhanced academic collaborations. Specifically, the introduction of flight routes leads to an increase in collaborations of at least 10.66%, while the establishment of HSR connections results in an increase by at least 32.65%. Flight routes are advantageous for facilitating collaborations in medium to long distances, while HSR primarily benefits medium to short-distance collaborations. Efficient public transportation connections, by reducing travel time, can significantly enhance collaboration across broader spatial areas within the knowledge production sector.