<p>Soil-rock mixtures (SRMs) exhibit complex shear mechanical properties and are widely distributed in geohazard-prone areas and major engineering sites. However, mesoscale investigations of SRMs and studies on soil-rock interfaces (SRI) shear failure behavior are limited by conventional apparatus precision. This study employs remolded millimeter-scale SRI specimens to clarify interface shear failure mechanisms. The natural morphology of pebbles is captured using the EinScan-Pro 3D scanner, and shear tests are conducted using a micrometer-resolution dual-lead-screw apparatus. Results indicate that pebble surfaces, while locally uneven, are generally flat. This characteristic significantly affects interface shear strength (the shear strength of the interface is positively correlated with the areal density of surface asperities) and induces fluctuations due to the alternating failure of different zones. On this basis, a shear model incorporating zone-specific failure modes (shear, sliding-shear, and tensile-shear) is established. The model accounts for the effects of natural morphology and the SRI compressive strength (<InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(JCS\)</EquationSource> <EquationSource Format="MATHML"><math> <mrow> <mi mathvariant="italic">JCS</mi> </mrow> </math></EquationSource> </InlineEquation>). The influence of these factors will be discussed in the following sections. The results demonstrate a model prediction mean relative error of approximately 3.59%. Natural morphology influences shear strength by modifying the morphological partition threshold (<InlineEquation ID="IEq2"> <EquationSource Format="TEX">\({\theta}_{part}^{*}\)</EquationSource> <EquationSource Format="MATHML"><math> <mmultiscripts> <mi>θ</mi> <mrow> <mi mathvariant="italic">part</mi> </mrow> <mrow> <mrow /> <mo>∗</mo> </mrow> </mmultiscripts> </math></EquationSource> </InlineEquation>) and the area proportions of failure regions. As the <InlineEquation ID="IEq3"> <EquationSource Format="TEX">\({\theta}_{part}^{*}\)</EquationSource> <EquationSource Format="MATHML"><math> <mmultiscripts> <mi>θ</mi> <mrow> <mi mathvariant="italic">part</mi> </mrow> <mrow> <mrow /> <mo>∗</mo> </mrow> </mmultiscripts> </math></EquationSource> </InlineEquation> decreases, the area of the shear failure region remains constant, while that of the sliding-shear region expands, thereby increasing the overall interface shear strength. Additionally, the interface shear strength decreases with increasing <InlineEquation ID="IEq4"> <EquationSource Format="TEX">\(JCS\)</EquationSource> <EquationSource Format="MATHML"><math> <mrow> <mi mathvariant="italic">JCS</mi> </mrow> </math></EquationSource> </InlineEquation>, the reduction is limited, as evidenced by a 31% increase in <InlineEquation ID="IEq5"> <EquationSource Format="TEX">\(JCS\)</EquationSource> <EquationSource Format="MATHML"><math> <mrow> <mi mathvariant="italic">JCS</mi> </mrow> </math></EquationSource> </InlineEquation> leading to only a 1.11% reduction in shear strength.</p>