The development of tin-lead alloyed halide perovskite nanocrystals (PNCs) is highly desirable for creating ultrastable, eco-friendly optoelectronic applications. However, the current incorporation of tin into the lead matrix results in severe photoluminescence (PL) quenching. To date, the precise atomic-scale structural origins of this quenching are still unknown, representing a significant barrier to fully realizing the potential of these materials. Here, we uncover the distinctive defect-related microstructures responsible for PL quenching using atomic-resolution scanning transmission electron microscopy and theoretical calculations. Our findings reveal an increase in point defects and Ruddlesden-Popper (RP) planar faults with increasing tin content. Notably, the point defects include a spectrum of vacancies and previously overlooked antisite defects with bromide vacancies and cation antisite defects emerging as the primary contributors to deep-level defects. Furthermore, the RP planar faults exhibit not only the typical rock-salt stacking pattern found in pure Pb-based PNCs but also previously undocumented microstructures rich in bromide vacancies and deep-level cation antisite defects. Direct strain imaging uncovers severe lattice distortion and significant inhomogeneous strain distributions caused by point defect aggregation, potentially breaking the local force balance and driving RP planar fault formation via lattice slippage. Our work illuminates the nature and evolution of defects in tin-lead alloyed halide perovskite nanocrystals and their profound impact on PL quenching, providing insights that support future material strategies in the development of less toxic tin-lead alloyed perovskite nanocrystals.