An apparatus for reconstructing digital video data stream reconstructs a transport stream from a first data stream and a second data stream. Both of the first data stream and the second data stream comprise a plurality of packets, a plurality of input stream time reference (ISCR) values, and a plurality of deleted null packet (DNP) values. The apparatus includes a packet interval detector, that estimates a packet interval according to the first data stream or the second data stream; an alignment unit, that generates an alignment signal according to the ISCR values and the packet interval; an oscillator, coupled to the packet interval detector, that generates an output pulse signal; and a reconstruction controller, that reconstructs the transport stream from the first data stream and the second data stream and outputs the transport stream according to the alignment signal and the output pulse signal. The alignment unit includes a fine tuner for fine tuning a frequency of the output pulse signal according to the ISCR values and a local count.