Layer‐by‐layer synthesis of surface‐coordinated metal–organic frameworks (SURMOF) enables the assembly of asymmetric, dipolar linkers into non‐centrosymmetric pillar‐layered structures. Using appropriate substrate terminations can yield oriented growth with the dipoles aligned perpendicular to the surface. The aligned pillar linkers give rise to a built‐in electrostatic field. In addition, the non‐centrosymmetric structure of the SURMOF gives rise to intriguing nonlinear optical features, such as second harmonic generation. Previous research with methyl‐functionalized bipyridine pillar linkers have demonstrated that this approach works in principle, but so far the total degree of alignment is only very small. Herein, a multiscale modelling approach is presented for in‐silico SURMOF assembly to identify and overcome limitations in the growth of pillar‐layered SURMOFs and to develop a strategy to maximize linker alignment. Using master equation models and kinetic Monte Carlo simulations, it is found that the formation of a highly ordered state corresponding to the thermodynamic equilibrium is often prevented by long‐lasting transient effects. Based on ab initio binding energies for a wide selection of hypothetical pillar linkers, a fast‐binding, slow‐relaxation scheme is able to be identified during the SURMOF growth for a range of different pillar linkers. These observations allow them to derive a rational strategy for the design of novel linkers to yield SURMOF‐based non‐centrosymmetric materials with substantially improved properties.