This study investigated the effects of long-term method of fertilization on growth and yield formation in early-season rice. Based on a 42-year field experiment initiated in 1981, three treatments: chemical N, P, and K (NPK), a double dose of chemical NPK (HNPK), and a combination of chemical and organic fertilizers (NPKM) were selected for comparison. Measurements included rice yield, yield components, tiller dynamic, dry matter accumulation, chlorophyll content (SPAD values), and transcriptome analysis of leaves at full heading stage in 2022. Results showed that rice yield followed the order NPKM >
HNPK >
NPK. The HNPK and NPKM treatments increased by 56.64% and 90.33%, respectively (p <
0.05). Spikelet density and 1000-grain weight increased by 9.16-22.89% and 3.74-4.28%, respectively. Both HNPK and NPKM enhanced the tillering rate by 43.84-72.73%, leading to an 18.95-57.54% increase in effective panicles. Dry matter accumulation from heading to filling stages was highest in NPKM-treated rice, with an increase of 3.31-4.25 g/plant in dry matter transport from leaves and stems to spikes during the filling to maturity stages. The SPAD values of NPKM-treated plants were consistently higher than those of HNPK and NPK treatments, with a smaller decline (6.94%) from heading to filling stages compared to 18.23% and 26.29% for HNPK and NPK, respectively. Correlation analysis indicated a positive relationship between yield and SPAD values or dry matter accumulation and a negative correlation with the decline in SPAD values from full heading to filling stage. Transcriptome analysis revealed significant enrichment of photosynthesis and plant senescence pathways among treatments. Overall, long-term combined application of chemical and organic fertilizers (NPKM) improved yield components, delayed chlorophyll degradation, promoted dry matter accumulation and transport, and regulated the expression of photosynthesis-related and senescence-related genes, ultimately optimizing growth and yield in early-season rice.