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Digitally‐encoded poly(phosphodiesters) (d‐PPDE) with highly complex primary structures are evaluated for layer‐by‐layer (LbL) assembly. To be easily decoded by mass spectrometry (MS), these digital polymers contain many different monomers: 2 coding units allowing binary encryption, 1 cleavable spacer allowing controlled MS fragmentation, and 3 mass tags allowing fragment identification. These complex heteropolymers are therefore composed of 6 different motifs. Despite this strong sequence heterogeneity, it is found that they enable a highly controlled LbL film formation. For instance, a regular growth is observed when alternating the deposition of negatively‐charged d‐PPDE and positively‐charged poly(allyl amine hydrochloride) (PAH). Yet, in this approach, the interdistance between consecutive coded d‐PPDE layers remains relatively small, which may be an issue for data storage applications, especially for the selective decoding of the stored information. Using poly(sodium 4‐styrene sulfonate) (PSS) as an intermediate non‐coded polyanion, it is shown that a controlled interdistance between d‐PPDE layers can be easily achieved, while still maintaining a regular LbL growth. Last but not least, it is found in this work that d‐PPDE of relatively small molecular weight (i.e., significantly smaller than those of PAH and PSS) still enables a controlled LbL assembly. [ABSTRACT FROM AUTHOR]