A semiconductor device has a TSV wafer and semiconductor die mounted over the TSV wafer. A channel is formed through the TSV wafer. An encapsulant is deposited over the semiconductor die and TSV wafer. Conductive TMV are formed through the encapsulant over the conductive TSV and contact pads of the semiconductor die. The conductive TMV can be formed through the channel. A conductive layer is formed over the encapsulant and electrically connected to the conductive TMV. The conductive TMV are formed during the same manufacturing process. An insulating layer is formed over the encapsulant and conductive layer. A plurality of semiconductor die of the same size or different sizes can be stacked over the TSV wafer. The plurality of semiconductor die can be stacked over opposite sides of the TSV wafer. An internal stacking module can be stacked over the semiconductor die and electrically connected through the conductive TMV.