Spot-size converter (SSC) is an essential building block for integrated photonic circuits applied as a mode transformer between optical components. One typical issue for SSC is the difficulty of broadening the vertical field profile. Herein, we propose a nanopixel SSC (1 × 2 μm2) with changing hole size and density. Unlike a typical SSC, this configuration controls both the lateral and vertical field profiles relatively easily by enhancing the nanopixel density. A vertical field expansion of 1.21 μm was obtained by enhancing the nanopixel density. In addition, we designed the optical field in the lateral direction using deep neural network (DNN)-based learning to realize a perfect circular spot for high coupling efficiency that reached -3 dB at λ0 = 1.572 μm when the optical field aspect ratio was adjusted to 1 after training for 200 epochs. Furthermore, the vertical expansion was increased from 1.21 to 4.9 μm and the coupling efficiency from -3 to -0.41 dB by combining it a silicon dioxide window structure (5 × 15 × 10 μm3). The 1-dB operating bandwidth of the designed SSC structure is 100 nm (1.5-1.6 μm), while fabrication tolerance of the nanopixels and window structure length for the designed SSC structure are ±15 nm and ±250 nm when the coupling efficiency drops by 1 dB.