Aiming to study the mechanical enhancement by the filler network in a rubber composite, three-dimensional images are acquired with in situ full field transmission X-ray microscopy (TXM), and the network structure of carbon black (CB) aggregates in a rubber matrix are studied with and without strain. Statistical analysis shows that the frequency of similar-sized aggregates decreases with the increase of aggregate size as well as the inter-aggregate distance monotonically without strain. An oscillation of the frequency-size plot is induced by strain on top of the damping trend, which is interpreted as stretch-induced breakage and re-aggregation of CB aggregates. Calculations adopting a soft-hard network model, predict a reduction of the contribution of the CB network to the mechanical property of the rubber composite by about 60%, caused by the breakage and re-aggregation of CB aggregates compared to those without strain. The experimental results directly prove the structural origin of the Payne effect and also show that TXM is a valuable tool to study the mechanical enhancement mechanism of filled rubber composites.