Surface‐enhanced Raman scattering (SERS) has received widespread attentions in biological detection since its single‐molecule sensitivity. The SERS substrate with numerous highly active hotspots can effectively capture target, whose precise fabrication is undoubtedly extremely challenging but attractive. Therefore, this work tries to achieve an ultrasensitive SERS platform based on the accurate regulations of its composition, structure, and distribution. Specifically, ordered CdS/MoS2@Au nanoparticles (AuNPs) nanopillars are fabricated by the aid of atomic layer deposition (ALD). Optimal selection and precise control of ALD cycles in MoS2 fabrication can accurately adjust the pillar diameter and obtain the most favorable minimum gap (8 nm) between pillars, which is advantageous to form multidimensional and high‐density hotspots thus generating a 9.4‐times promotion as compared with the control group. On the other hand, calculated analysis shows that appropriate spacing distance between pillars slightly larger than analyte molecule can produce considerable capillary force, which is advantageous to capture analyte and anchor it in the high‐charged‐density region for higher self‐activation of hotpots. Based on the above two favorable factors, a linear detection window from 10 × 10−18 to 1 × 10−8 m with an ultralow detection limit of 0.82 × 10−18 m for miRNA‐182 is achieved.