We have proposed a new multichip-to-wafer 3D stacking method with high throughput and high yield based on a capillary self-assembly method using liquid droplets. In this paper, we optimized conditions in self-assembly and microbump bonding using non-conductive film (NCF)-covered known good dies (KGDs). Self-assembly of the NCF-covered KGDs provided high chip alignment accuracy within approximately 1 μm. After the self-assembly and a subsequent thermal compression, resultant microbump chains composed of over 7,000 microbump joints exhibited good electrical properties of 32 mω/joint without bridge short and open failures. The microbump joint resistance varied within 5% of the initial values after thermal cycle test (TCT) of 1,000 cycles. In addition, we demonstrated a multi-layer 3D stacking by the self-assembly method with the NCF-covered KGDs.