Polymer conjugation is an attractive approach for delivering insoluble and highly toxic drugs to tumors. However, most reports in the literature only disclose the optimal composition without emphasizing rational design or composition optimization to achieve maximized biological effects. In this study, we aimed to demonstrate that composition of a polymer conjugate would determine its physiochemical characteristics, tumor penetration, and, ultimately, the in vivo efficacy. We also aimed to examine whether the tumor spheroid model could generate comparable results with the in vivo tumor model in terms of tumor penetration and efficacy of the various polymer conjugates. We have designed a polymer conjugate delivery system for a chemotherapeutic drug podophyllotoxin (PPT) by covalently conjugating PPT and polyethylene glycol (PEG) with acetylated carboxymethyl cellulose to yield conjugates containing various amounts of PPT and PEG. Depending on the composition, these conjugates self-assembled into nanoparticles (NPs) with different physicochemical properties. Conjugates with an increased PPT content formed particles with an increased diameter. In the present study, we selected three conjugates representing compositions containing high, medium, and low drug content, and compared their particle formation, drug release kinetics, their ability to penetrate tumor spheroid and in vivo s.c. tumor, and finally their antitumor efficacy in spheroid culture and an in vivo s.c. tumor model. We found that the low drug content conjugate formed smaller NPs (20 nm) compared to the high drug content conjugates (30–120 nm), and displayed faster drug release kinetics (5%/day vs 1–3%/day), improved tumor penetration, and enhanced antitumor efficacy in both the spheroid model and s.c. tumor model. In particular, the low drug content conjugate preferentially accumulated in the hypovascular region within the tumor, inducing complete regression of s.c. tumors and the metastasis to the lungs. Our data indicate composition optimization is needed to select the optimal conjugate, and tumor spheroid culture is a robust screening tool to help select the optimal formulation.