In this article, the indentation creep characteristics and the microstructures are assessed for the friction stir welded modified 9Cr-1Mo steel and LN-type 316 SS dissimilar joint. Microstructures are characterized for the post-weld heat treated and indentation crept samples at different conditions with optical microscopy, scanning electron microscope and energy dispersive X-ray spectroscopy. Distinct heat-affected zones were revealed with the refined and reformed martensite (α′) and austenite (γ) structures that formed in view of the distinct thermal conductivity property and the differences in lower critical(Ac1) and upper critical(Ac3) transformation temperatures. The size of prior austenite grain sizes was found to be varied significantly at the different regions. Indentation creep data were acquired in distinct weld zones at 873, 898 and 923 K. Zone-wise indentation depth, steady-state creep behaviour (SSCR) and activation energy ( Q) were evaluated and correlated with the microstructures. The formation of small prior austenitic grain (PAG) structures and the grain boundary vacancies has led to maximum creep deformation (86.83%) at the heat affected zone of the modified 9Cr-1Mo steel. Furthermore, the reduction in lath structures and the formation of tiny α′ with soft substructures have lowered the hardness values to around 210  ±  21 HV, which is 20 HV less than the post weld heat treated sample. In the stir zone, the presence of dynamically refined and rich γ along with fine α′ layers has improved the steady-state creep rate of 9.112 E-7, which is less than the modified 9Cr-1Mo steel and the heat affected zone at modified 9Cr-1Mo side. The coarse austenite structures that existed in the LN-type 316 base metal have resisted more creep damage and exhibited high activation energy (i.e. 490 kJ mol−1) than the stir zone and heat affected zone of the LN-type 316 SS.