Interactions among large number of entities is naturally high-dimensional and incomplete (HDI) in many big data related tasks. Behavioral characteristics of users are hidden in these interactions, hence, effective representation of the HDI data is a fundamental task for understanding user behaviors. Latent factor analysis (LFA) model has proven to be effective in representing HDI data. The performance of an LFA model relies heavily on its training process, which is a non-convex optimization. It has been proven that incorporating local curvature and preprocessing gradients during its training process can lead to superior performance compared to LFA models built with first-order family methods. However, with the escalation of data volume, the feasibility of second-order algorithms encounters challenges. To address this pivotal issue, this paper proposes a mini-block diagonal hessian-free (Mini-Hes) optimization for building an LFA model. It leverages the dominant diagonal blocks in the generalized Gauss-Newton matrix based on the analysis of the Hessian matrix of LFA model and serves as an intermediary strategy bridging the gap between first-order and second-order optimization methods. Experiment results indicate that, with Mini-Hes, the LFA model outperforms several state-of-the-art models in addressing missing data estimation task on multiple real HDI datasets from recommender system. (The source code of Mini-Hes is available at https://github.com/Goallow/Mini-Hes)