Development of high-performance photoinitiator is the key to enhance the printing speed, structure resolution and product quality in 3D laser printing. Here, to improve the printing efficiency of 3D laser nanoprinting, we investigate the underlying photochemistry of gold and silver nanocluster initiators under multiphoton laser excitation. Experimental results and DFT calculations reveal the high cleavage probability of the surface S-C bonds in gold and silver nanoclusters which generate multiple radicals. Based on this understanding, we design several alkyl-thiolated gold nanoclusters and achieve a more than two-orders-of-magnitude enhancement of photoinitiation activity, as well as a significant improvement in printing resolution and fabrication window. Overall, this work for the first time unveils the detailed radical formation pathways of gold and silver nanoclusters under multiphoton activation and substantially improves their photoinitiation sensitivity via surface engineering, which pushes the limit of the printing efficiency of 3D laser lithography.