Superconducting tunnel junction (STJ) array detectors can exhibit excellent performance with respect to energy resolution, detection efficiency, and counting rate in the soft X-ray energy range, by which those excellent properties STJ array detectors are well suited for detecting X-rays at synchrotron radiation facilities. However, in order to achieve a high throughput analysis for trace impurity elements such as dopants in structural or functional materials, the sensitive area of STJ array detectors should be further enlarged up to more than 10 times larger by increasing the pixel number in array detectors. In this work, for a large STJ-pixel number of up to 1000 within a 10,mm- square compact chip, we have introduced three-dimensional (3D) structure by embedding a wiring layer in a SiO$_{2}$ isolation layer underneath a base electrode layer of STJs. The 3D structure is necessary for close-packed STJ arrangement, avoiding overlay of lead wiring, which is common in conventional two-dimensional layout. The fabricated STJ showed excellent current-voltage characteristics having low subgap currents less than 2,nA, which are the same as those of conventional STJs. An STJ pixel has an energy resolution of 31,eV (FWHM) for C-K$alpha $ (277,eV).