This work focused on the effects of compatibility techniques [i.e., modification of filler and addition of an l‐lysine diisocyanate (LDI) coupling agent] and filler content on the properties of bio‐nanocomposite films prepared using poly(butylene succinate) (PBS) as a matrix and starch nanocrystals (SNC) as filler by chill‐roll cast film extrusion. The films reinforced with modified SNC had superior tensile and barrier properties than those reinforced with unmodified SNC or an added LDI. Elongation at break of 1%wt modified SNC/PBS film was increased up to 51.1% compared with neat PBS film. Water vapor transmission rate and oxygen transmission rate values of 9%wt modified SNC/PBS film (54.1 g m−2 day and 216.3 cc m−2 day) were lower than those of neat PBS film (114.5 g m−2 day and 560.3 cc m−2 day) due to the higher hydrophobicity and better dispersion of modified SNC in PBS leading to the superior properties of PBS films. The PBS bio‐nanocomposite films can be completely degraded within ~3 months under wastewater treatment condition. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018, 135, 46836.