In this paper, we propose a new R/D estimation method for intra-predictive coding with deep block partitioning structures. In our proposed R/D prediction, we adopt a particle filtering based prediction (PFP) to precisely predict intermediate R/D estimates for the next frame in a stochastic manner, which helps increasing the prediction accuracy of fast changing R/D values. Then, based on the intermediate R/D estimates by PFP, we infer an optimal model parameter of the TC’s probability density function (pdf) via convex optimization. We found that the proposed method brings about more stable R/D estimation performance thanks to both the improved prediction accuracy using the PFP for abrupt changes in true R/D values and the precise estimation of the optimal model parameter. Experimental results show that our method significantly reduces the normalized root mean square error from average 3.17 to 0.79 (74.90% reduction) for rate and from average 2.32 to 0.82 (64.61% reduction) for distortion, compared to the state-of-the art method.