Emerging Markets (EMs) are fundamentally reliant on high-growth innovation ecosystems to achieve national objectives, such as India’s vision for Viksit Bharat 2047. India, currently the third largest startup ecosystem globally, serves as a critical model for this developmental imperative. However, this ecosystem presents a paradox: immense scale and ambition are juxtaposed against acute structural fragility, evidenced by a persistent non-survival rate exceeding 90% within the first five years of operation. This paper systematically dissects this duality, employing an Interpretative Structural Modeling (ISM) framework to expose the core dependencies within the ecosystem. The analysis confirms a rigid hierarchy: governmental Academic Regulations act as the Apex Constraint (Level 4, Maximum Driving Power), while Incubation is the highly dependent foundational output (Level 1, Maximum Dependence Power).Crucially, the study diagnoses the operational crisis of Product-Market Fit (P-M Fit) failure, accounting for 34% of shutdowns, linking this to systemic deficiencies in the interdependent operational core (Level 2: Mentorship, Networks, and Funding). We analyze the dual-layered financial architecture of the Government of India, including the macro-level ₹10,000 crore Fund of Funds and the micro-level ₹945 crore Startup India Seed Fund Scheme (SISFS). Based on the structural dependencies revealed, this research proposes a strategic shift: focusing resources not merely on capital volume, but on mitigating the identified structural and operational risks. Recommendations center on Apex-level regulatory streamlining, targeted capital deployment for P-M Fit validation, leveraging Digital Public Infrastructure (DPI) for inclusive scale, and mandating Gender and Social Inclusion (GESI) alignment. The findings offer a transferable blueprint for other EMs seeking to convert extensive, fragile growth into intensive, resilient vitality.