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As a significant Alzheimer’s disease (AD)-specific biomarker, the examination of brain-derived tau (BD-tau) is significant in terms of the diagnosis and differentiation of neurological disorders. In this research, sea urchin-like MoSe2 microspheres were synthesized by hydrothermal synthesis, revealing significant SERS activity, and the enhancement factor (EF) reached 1.44 × 107. The remarkable EF was mainly ascribed to the (i) charge transfer between MoSe2 and MB, (ii) MB molecule’s resonance effect, and (iii) molecular enrichment of porous structures. Through an aptamer-antibody sandwich method, we prepared a BD-tau SERS detection platform based on sea urchin-like MoSe2 microspheres. The liner range was 0.05–200.00 pM with a limit of detection (LOD) as low as 0.028 pM. Besides, the developed detection platform demonstrated excellent selectivity and enabled early diagnosis of AD patients. In general, the MoSe2 SERS detection platform can well detect the concentration of BD-tau in mouse plasma samples, showing great potential in specific recognition of AD among neurodegenerative diseases.