The effects of long-term nutrient deficiency on cassava agronomic characters, yield and starch content were studied to provide scientific basis for fertilization of continuous cropping. In this study, experimental materials in 2019 to 2021 (continuous cropping in 28th-30th years) were selected from the time axis of long-term fertilization trials. CK (with NPK), –N (without N), –P (without P), –K (without K) combined with two cassava varieties SC205 and SC124 were selected. The SPAD value, plant height, stem diameter and starch content, yield, starch yield of the fresh storage root (FSR) were measured and evaluate. Compared to CK, –N and –K significantly reduced plant height, and –N, –P and –K significantly reduced stem diameter of cassava. Meanwhile, –K significantly reduced SPAD value of leaves. Test of between-subjects effect showed that, variety or fertilization had significant effects on agronomic characters, but the interaction effect between them was not significant. The starch content of FSR, compared to CK, –N significantly improved in 2021. –K significantly reduced, the three-year average decrease was 14.2%. Compared to CK, –N, –P and –K significantly reduced the yield, starch yield of FSR, storage root number per plant (SRNPP) and weight per storage root (WPSR). The yield of FSR reduced by more than 40.0% under different nutrient deficiency, while the yield effects were insignificantly different among nutrient deficiency treatments. The starch yield of FSR under -K decreased by 53.3%, the decrease was significantly higher than that of –N and –P. The correlation analysis showed that yield, starch yield of FSR were extremely significantly positively correlated with the SRNPP, and significantly positively correlated with the WPSR. –N, –P and –K significantly inhibited cassava growth. N was the primary limiting factor for cassava fresh storage root yield in the early stage of continuous cropping, followed by K, but P effect was not obvious. With the extension of continuous cropping years, the effects of K and P effect gradually became more significant, and N, K became the main limiting factors, then there was no significant difference on the fresh storage root yield effect among N, P and K, there were equally important.