Superconducting-tunnel-junction (STJ) array X-ray detectors have exhibited excellent characteristics for fluorescence-yield X-ray absorption fine structure (XAFS) in a soft X-ray range. For high-throughput XAFS analyses, we developed a new close-packed STJ arrangement with a space of 10 m (use the correct space) between adjacent STJ pixels by using three-dimensional multilayer structure (3D-STJ) with the wiring layer underneath the STJ pixel layer. In this work, in order to solve a double-peak response originating from absorption events in the top and bottom electrodes, we have fabricated the 3D-STJ with an asymmetric layer structure. Single-peak response for the soft X-rays below 0.7 keV was obtained. The closed-packed 3D-STJ array detector with 100 pixels has an operation yield of 93 % and a mean energy resolution of 12.5 0.7 eV in full-width at half-maximum for the C-K X-ray.