Flattened carbon nanotubes (flCNTs) are a primary component of many carbon nanotube (CNT) yarn and sheet materials, which are promising reinforcements for the next generation of ultra-strong composites for aerospace applications. Significant improvements in the performance of CNT materials can be realized with improvements in the load transfer between flCNTs, which are generally oriented at different angles with respect to each other. An intriguing approach to improving the load transfer is via irradiation-induced chemical crosslinking between adjacent flCNTs. The objective of this research is to use molecular dynamics (MD) simulations to predict the behavior of flCNT junctions with 0- and 90-degree orientations and varying levels of crosslinking. The results indicate that crosslinking improves the flCNT interfacial load transfer for both orientations, but degrades the flCNT tensile response. The primary toughening mechanism at the flCNT/flCNT interface is the formation of carbon chains that provide load transfer up to the point of total rupture. Based on these results, it is clear that irradiation-induced crosslinking is beneficial in CNT-based composite systems in which interfacial load transfer between flCNTs is of primary importance, even though individual flCNTs may lose some mechanical integrity with crosslinking.