Mixing of a gravity flow with substrate over which it travels can control flow transformations with implications for the structure of the deposit that is left; however, the effects of mixing in conglomerate-dominated gravelly underflow in lacustrine environments remain poorly understood. This study documents two types of interactions between gravelly underflow and substrate and the resulting conglomerate deposits across a lacustrine fan-delta system in the Junggar Basin, northwest China. The resulting conglomerates are typically massive, poorly sorted, clast-supported without reserve grading; rich in mudstone clasts; and having been emplaced by river-derived hyperpycnal flow. Based on the character of the matrices between the clasts, conglomerates are divided into three sub-categories: (i) muddy (mud-rich) conglomerates with a mainly fine-grained muddy matrix, (ii) sandy (mud-poor) conglomerates with a mainly sandy matrix, and (iii) mud-bearing sandy conglomerates with a coexisting mud-sand matrix. Furthermore, two distinct lithological associations were identified: (i) a regularly recurring tripartite conglomerate unit interlayered with mudstone (S I) and (ii) a regularly recurring tripartite conglomerate unit interlayered with sandstone (S II). Both lithological associations contained a recurring tripartite conglomerate unit with a basic tripartite structure consisting of muddy conglomerates in the lower division, mud-bearing sandy conglomerates in the middle division, and sandy conglomerates in the upper division. There was more sand in the upper layers of the tripartite conglomerate unit matrix. Muddy conglomerates with large amount of mudstone clasts are thought to form through extensive erosion and mixing between the lower part of the flow with mud-substrate on the lake bottom, whereas central mud-bearing conglomerates and upper sandy conglomerates are considered to be generated by successively weaker mixing in the upper part of the flow. The consequent sandy trailing flow resting upon the previously-emplaced tripartite conglomerate unit forms a thinner sandstone bed that acts as a “sand mat” for the next incoming gravelly flow. A single sandy conglomerate bed subsequently forms above when gravel mixes with the sand substrate, as opposed to forming muddy conglomerates that were generated by mud from eroded substrate. Our results show that the erosion and mixing of sediment flow with substrate are important factors in flow transformation and deposition and that the substrate type (muddy or sandy) along the flow path plays a crucial role in controlling flow behavior and reservoir characteristics.