Abstract: Using the latest second-generation Cunninghamia lanceolate hybrids (Long 15×1339), HF1(3 super-parent hybrids), LF2( 3 low-parent hybrids) and parents (P1 and P2),all sample groups were compared by transcriptome sequencing. The result demonstrated that in a total of 12 samples, 5.8E+08 Clean reads were generated by transcriptome sequencing, and the total length was 49 803 726nt. BLASTX analysis was performed on Clean reads in six databases (Nr, Swiss-prot, KOG, KEGG, Pfam, GO), through sequence alignment which resulted in 80 171 unigenes. Analysis indicated that the productivity of C.lanceolata hyhybrids associated to the following factors, growth of progenies in cross combination ssegregated, growth of HF1 faster than that of LF2, which was due to the uneven and unbalanced distribution of expression unigeneattwo-level: among GO and KEGG terms and within GO and KEGG terms. The differential genes of GO and KEEG terms in high parental generation were not evenly distributed and balanced; The distribution of the difference genes of GO terms and KEEG terms in the low parental generation tends to be uniform and balanced.