A silicon based substrate includes a silicon wafer, a first circuit substrate and a second circuit substrate. The silicon wafer includes a first surface and a second surface and at least a through silicon via. The first circuit substrate is disposed on the first surface and includes a plurality of first dielectric layers and a plurality of first conductive trace layers alternately stacked. The second circuit substrate is disposed on the second surface and includes a plurality of second dielectric layers and a plurality of second conductive trace layers alternately stacked. The trace density of the first conductive trace layers is higher than the trace density of the second conductive trace layers. Otherwise, the first dielectric layer includes an inorganic material and the second dielectric layer includes an organic material. A manufacturing method of the silicon based substrate is also provided.